aTyr Pharma (ATYR) 10-K 26 Mar 20 2019 FY Annual report Financial data

Document and Entity Information

Document and Entity Information - USD ($)	12 Months Ended
	Dec. 31, 2019	Mar. 19, 2020	Jun. 28, 2019
Cover [Abstract]
Document Type	10-K
Amendment Flag	false
Document Period End Date	Dec. 31, 2019
Document Fiscal Year Focus	2019
Document Fiscal Period Focus	FY
Trading Symbol	LIFE
Entity Registrant Name	aTYR PHARMA INC
Entity Central Index Key	0001339970
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Non-accelerated Filer
Entity Small Business	true
Entity Emerging Growth Company	true
Entity Ex Transition Period	true
Entity Shell Company	false
Entity Common Stock, Shares Outstanding		9,352,498
Entity Public Float			$ 10,206,392
Document Annual Report	true
Document Transition Report	false
Entity File Number	001-37378
Entity Incorporation, State or Country Code	DE
Entity Tax Identification Number	20-3435077
Entity Address, Postal Zip Code	92121
City Area Code	858
Local Phone Number	731-8389
Entity Address, Address Line One	3545 John Hopkins Court
Entity Address, Address Line Two	Suite #250
Entity Address, City or Town	San Diego
Entity Address, State or Province	CA
Security Exchange Name	NASDAQ
Title of 12(b) Security	Common Stock, par value $0.001 per share
Entity Interactive Data Current	Yes
Documents Incorporated by Reference	Portions of the registrant’s proxy statement to be filed with the Securities and Exchange Commission (SEC), pursuant to Regulation 14A in connection with the registrant’s 2020 Annual Meeting of Stockholders, which will be filed subsequent to the date hereof, are incorporated by reference into Part III of this annual report on Form 10-K. Such proxy statement will be filed with the SEC not later than 120 days following the end of the registrant’s fiscal year ended December 31, 2019

Consolidated Balance Sheets

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Current assets:
Cash and cash equivalents	$ 9,210	$ 22,962
Available-for-sale investments, short-term	21,934	26,583
Prepaid expenses and other assets	781	1,258
Total current assets	31,925	50,803
Property and equipment, net	1,270	1,853
Right-of-use assets	2,821
Other assets	172	90
Total assets	36,188	52,746
Current liabilities:
Accounts payable	847	1,040
Accrued expenses	2,376	2,026
Contract liability	208
Current portion of operating lease liability	755
Current portion of long-term debt, net of issuance costs and discount	8,737	7,767
Total current liabilities	12,923	10,833
Long-term operating lease liability, net of current portion	2,239
Long-term debt, net of current portion and issuance costs and discount		8,263
Commitments and contingencies (Note 6)
Stockholders’ equity:
Preferred stock, $0.001 par value per share; 5,000,000 undesignated authorized shares; Class X Convertible Preferred Stock issued and outstanding shares – 1,643,961 and 2,285,952 as of December 31, 2019 and 2018, respectively	2	2
Common stock, $0.001 par value per share; 10,714,286 authorized shares; issued and outstanding shares – 3,891,787 and 2,186,389 as of December 31, 2019 and 2018, respectively	4	2
Additional paid-in capital	343,524	332,407
Accumulated other comprehensive loss	(40)	(60)
Accumulated deficit	(322,304)	(298,701)
Total aTyr Pharma stockholders’ equity	21,186	33,650
Noncontrolling interest in Pangu BioPharma Limited	(160)
Total stockholders' equity	21,026	33,650
Total liabilities and stockholders’ equity	$ 36,188	$ 52,746

Consolidated Balance Sheets (Pa

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2019	Dec. 31, 2018
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000,000	5,000,000
Common stock, par value	$ 0.001	$ 0.001
Common stock, shares authorized	10,714,286	10,714,286
Common stock, shares issued	3,891,787	2,186,389
Common stock, shares outstanding	3,891,787	2,186,389
Class X Convertible Preferred Stock [Member]
Preferred stock, shares issued	1,643,961	2,285,952
Preferred stock, shares outstanding	1,643,961	2,285,952

Consolidated Statements of Oper

Consolidated Statements of Operations - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Revenues:
Total revenues	$ 422
Operating expenses:
Research and development	14,048	$ 20,385	$ 30,067
General and administrative	9,352	12,435	17,078
Total operating expenses	23,400	32,820	47,145
Loss from operations	(22,978)	(32,820)	(47,145)
Total other expense, net	(785)	(1,695)	(1,062)
Consolidated net loss	(23,763)	(34,515)	(48,207)
Net loss attributable to noncontrolling interest in Pangu BioPharma Limited	160
Net loss attributable to aTyr Pharma, Inc.	$ (23,603)	$ (34,515)	$ (48,207)
Net loss per share attributable to common stockholders, basic and diluted	$ (7.03)	$ (16.11)	$ (26.13)
Weighted average common stock shares outstanding, basic and diluted	3,355,600	2,141,961	1,845,033
Collaboration Revenue [Member]
Revenues:
Total revenues	$ 422

Consolidated Statements of Comp

Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Statement Of Income And Comprehensive Income [Abstract]
Consolidated net loss	$ (23,763)	$ (34,515)	$ (48,207)
Other comprehensive gain (loss):
Change in unrealized gain (loss) on available-for-sale investments, net of tax	20	60	(44)
Comprehensive loss	(23,743)	(34,455)	(48,251)
Comprehensive loss attributable to noncontrolling interest Pangu BioPharma Limited	160
Comprehensive loss attributable to aTyr Pharma, Inc. common stockholders	$ (23,583)	$ (34,455)	$ (48,251)

Consolidated Statements of Stoc

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Convertible Preferred Stock [Member]	Common Stock [Member]	Additional Paid-In Capital [Member]	Other Comprehensive Gain/(Loss) [Member]	Accumulated Deficit [Member]	Noncontrolling Interest [Member]
Beginning balance at Dec. 31, 2016	$ 62,801		$ 2	$ 278,854	$ (76)	$ (215,979)
Beginning balance, Shares at Dec. 31, 2016			1,698,252
Exercise of common stock options and release of restricted stock units	186			186
Exercise of common stock options and release of restricted stock units, Shares			7,914
Issuance of common stock pursuant to employee stock purchase plan	175			175
Issuance of common stock pursuant to employee stock purchase plan, Shares			4,364
Issuance of common stock and preferred stock from private placement, net of offering costs	42,239	$ 2		42,237
Issuance of common stock and preferred stock from private placement, net of offering costs, Shares		2,285,952	419,438
Issuance of warrants related to term loan	263			263
Changes in share repurchase liability	48			48
Stock-based compensation	6,784			6,784
Net unrealized gain (loss) on investments, net of tax	(44)				(44)
Net loss	(48,207)					(48,207)
Ending balance at Dec. 31, 2017	64,245	$ 2	$ 2	328,547	(120)	(264,186)
Ending balance, Shares at Dec. 31, 2017		2,285,952	2,129,968
Consolidated net loss	(48,207)
Exercise of common stock options and release of restricted stock units	14			14
Exercise of common stock options and release of restricted stock units, Shares			3,670
Issuance of common stock pursuant to employee stock purchase plan	36			36
Issuance of common stock pursuant to employee stock purchase plan, Shares			3,028
Issuance of common stock from at the market offerings, net of offering costs	379			379
Issuance of common stock from at the market offerings, net of offering costs, Shares			49,723
Stock-based compensation	3,431			3,431
Net unrealized gain (loss) on investments, net of tax	60				60
Net loss	(34,515)					(34,515)
Ending balance at Dec. 31, 2018	33,650	$ 2	$ 2	332,407	(60)	(298,701)
Ending balance, Shares at Dec. 31, 2018		2,285,952	2,186,389
Consolidated net loss	(34,515)
Ending balance at Dec. 31, 2018	33,650
Conversion of preferred stock to common stock, shares		(641,991)	229,283
Issuance of common stock upon release of restricted stock units, Shares			7,487
Issuance of common stock pursuant to employee stock purchase plan	13			13
Issuance of common stock pursuant to employee stock purchase plan, Shares			3,117
Issuance of common stock from at the market offerings, net of offering costs	4,405		$ 1	4,404
Issuance of common stock from at the market offerings, net of offering costs, Shares			805,357
Issuance of common stock from registered direct offering, net of offering costs	4,918		$ 1	4,917
Issuance of common stock from registered direct offering, net of offering costs, Shares			660,154
Stock-based compensation	1,783			1,783
Net unrealized gain (loss) on investments, net of tax	20				20
Net loss	(23,603)
Ending balance at Dec. 31, 2019	21,186
Ending balance, Shares at Dec. 31, 2019		1,643,961	3,891,787
Consolidated net loss	(23,763)					(23,603)	$ (160)
Ending balance at Dec. 31, 2019	$ 21,026	$ 2	$ 4	$ 343,524	$ (40)	$ (322,304)	$ (160)

Consolidated Statements of Cash

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Cash flows from operating activities:
Consolidated net loss	$ (23,763)	$ (34,515)	$ (48,207)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	635	746	713
Stock-based compensation	1,783	3,431	6,784
Debt discount accretion and non-cash interest expense	707	966	590
Amortization (accretion) of premium (discount) of available-for-sale investment securities	(284)	(261)	14
Amortization of right-of-use assets	731
(Gain) loss on disposal of property and equipment	(28)	18
Deferred rent			(130)
Changes in operating assets and liabilities
Prepaid expenses and other assets	334	610	761
Accounts payable and accrued expenses	162	(2,058)	(2,889)
Contract liability	208
Operating lease liability	(498)
Net cash used in operating activities	(20,013)	(31,063)	(42,364)
Cash flows from investing activities:
Purchases of property and equipment	(79)	(594)	(1,312)
Purchases of available-for-sale investment securities	(40,647)	(40,299)	(77,672)
Maturities of available-for-sale investment securities	45,600	78,065	51,347
Proceeds from sale of property and equipment	51
Net cash provided by (used in) investing activities	4,925	37,172	(27,637)
Cash flows from financing activities:
Proceeds from issuance of common stock through employee stock purchase plan	13	36	175
Proceeds from issuance of common stock through option exercises and release of restricted stock units		14	186
Proceeds from issuance of common stock through at the market offerings, net of offering costs	4,405	379
Proceeds from issuance of common stock through registered direct offering, net of offering costs	4,918
Proceeds from issuance of securities in the Private Placement, net of issuance costs			42,477
Proceeds from borrowing, net			9,866
Repayments on borrowings	(8,000)	(4,667)
Net cash provided by (used in) financing activities	1,336	(4,238)	52,704
Net change in cash and cash equivalents	(13,752)	1,871	(17,297)
Cash and cash equivalents at beginning of period	22,962	21,091	38,388
Cash and cash equivalents at the end of period	9,210	22,962	21,091
Supplemental disclosure of cash flow information:
Interest paid	$ 1,122	1,700	1,000
Purchase of fixed assets included in accounts payable		$ 4	260
Supplemental schedule of noncash investing and financing activities:
Issuance of warrants in connection with borrowings			263
Changes in share repurchase liability			$ 48

Organization, Business and Basi

Organization, Business and Basis of Presentation	12 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Organization, Business and Basis of Presentation	1. Organization, Business and Basis of Presentation Organization and Business We were incorporated in the state of Delaware on September 8, 2005. We are focused on the discovery and development of innovative medicines based on novel immunological pathways. Principles of Consolidation Our consolidated financial statements include our accounts and our 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma Limited (Pangu BioPharma). All intercompany transactions and balances are eliminated in consolidation. Reverse Stock Split In June 2019, we filed a Certificate of Amendment to our Restated Certificate of Incorporation with the Secretary of State of the State of Delaware to effect a 1-for-14 reverse stock split of our issued and outstanding common stock. The reverse stock split became effective at 5:00 p.m. Eastern Time on June 28, 2019 and our common stock began trading on a split-adjusted basis on The Nasdaq Capital Market on July 1, 2019. Our consolidated financial statements and these notes give retrospective effect to the reverse stock split for all periods presented. All issued and outstanding common stock, options and warrants exercisable for common stock, restricted stock units, preferred stock conversions to common stock and per share amounts contained in our consolidated financial statements have been retrospectively adjusted. Liquidity and Financial Condition We have incurred losses and negative cash flows from operations since our inception. As of December 31, 2019, we had an accumulated deficit of $322.3 million and we expect to continue to incur net losses for the foreseeable future. As of December 31, 2019, our cash, cash equivalents and available-for-sale investments were $31.1 million. Since that time, we received $8.0 million related to the Kyorin Agreement and approximately $20.7 million in gross proceeds from our underwritten follow-on public offering of common stock, before deducting underwriting discounts, commissions and offering expenses payable by us. We believe that our current cash, cash equivalents and available-for-sale investments, will be sufficient to meet our anticipated cash requirements for a period of at least one year from the date of this Annual Report. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years at a minimum. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. Accordingly, we will need to raise substantial additional capital to fund our operations. The amount and timing of our future funding requirements will depend on many factors, including the pace and results of our preclinical and clinical development efforts and the timing and nature of the regulatory approval process for our product candidates. We anticipate that we will seek to fund our operations through equity offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and when we are closer to commercialization of our product candidates potentially through debt financings. However, we may be unable to raise additional capital or enter into such arrangements when needed on favorable terms or at all. Our failure to raise capital or enter into such arrangements when needed would have a negative impact on our financial condition and ability to develop our product candidates. In May 2018, we implemented a corporate restructuring and program prioritization plan (Restructuring Plan) to streamline our operations and concentrate development efforts on the advancement of our therapeutic candidate, ATYR1923. In connection with the Restructuring Plan, we reduced our workforce by approximately 30% to 42 full-time employees. We completed the workforce reduction in June 2018. Use of Estimates Our consolidated financial statements are prepared in accordance with generally accepted accounting principles (GAAP). The preparation of our consolidated financial statements requires us to make estimates and assumptions that impact the reported amounts of assets, liabilities and expenses and the disclosure of liabilities in our consolidated financial statements and accompanying notes. The most significant estimates in our consolidated financial statements relate to the fair value of equity issuances and awards, and clinical trial and research and development expenses. Although these estimates are based on our knowledge of current events and actions we may undertake in the future, actual results may ultimately differ materially from these estimates and assumptions. Segment Reporting Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision-maker in making decisions regarding resource allocation and assessing performance. We view our operations and manage our business in one operating segment. Reclassifications Certain reclassifications have been made to prior year amounts to conform to the current year presentation. The reclassifications were not material to the consolidated financial statements.

Summary of Significant Accounti

Summary of Significant Accounting Policies	12 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Summary of Significant Accounting Policies	2. Summary of Significant Accounting Policies Cash and Cash Equivalents Cash and cash equivalents consist primarily of readily available checking, money market accounts and money market funds. We consider all highly liquid investments that mature in three months or less when purchased to be cash equivalents. Investment Securities Investment securities primarily consist of investment grade corporate debt securities, asset-backed securities, commercial paper and United States Treasury securities. We classify all investment securities as available-for-sale. Investment securities are carried at fair value, with the unrealized gains and losses, if any, reported as a component of other comprehensive income (loss) in stockholders’ equity until realized. Realized gains and losses from the sale of investment securities, if any, are determined on a specific identification basis. A decline in the market value of any investment security below cost that is determined to be other than temporary will result in an impairment charge to earnings and a new cost basis for the security is established. No such impairment charges were recorded for any period presented. Premiums and discounts are amortized or accreted over the life of the related security as an adjustment to yield using the straight-line method and are included in interest income. Interest income is recognized when earned. As of December 31, 2019, we held an aggregate total of $21.9 million of investment securities which consisted of corporate debt securities, asset-backed securities, and commercial paper all of which will mature in less than one year, and there was an unrealized gain of $8,500 between the amortized cost and fair value of these investment securities. As of December 31, 2018, we held $26.6 million of corporate debt securities, asset-backed securities and United States Treasury securities, all of which mature in less than one year, and there was an unrealized loss of $10,000 between the amortized cost and fair value of these investment securities. Concentration of Credit Risk Financial instruments that potentially subject us to significant concentration of credit risk consist primarily of cash, cash equivalents and investment securities. We have established guidelines regarding diversification of investments and their maturities, which are designed to maintain principal and maximize liquidity. We maintain deposits in federally insured financial institutions in excess of federally insured limits. We have not experienced any losses in such accounts and we believe that we are not exposed to significant credit risk due to the financial position of the depository institutions in which those deposits are held. Property and Equipment Property and equipment are stated at cost and depreciated on a straight-line basis over the estimated useful life of the related assets (generally three to seven years). Leasehold improvements are stated at cost and amortized on a straight-line basis over the lesser of the remaining term of the related lease or the estimated useful life of the leasehold improvements. Repairs and maintenance costs are charged to expense as incurred . Impairment of Long-Lived Assets Long-lived assets consist primarily of property and equipment. An impairment loss is recorded if and when events and circumstances indicate that assets might be impaired and the undiscounted cash flows estimated to be generated by those assets are less than the carrying amount of those assets. While our current and historical operating losses are indicators of impairment, we believe that future cash flows to be received support the carrying value of our long-lived assets and, accordingly, have not recognized any impairment losses since inception. Accrued Expenses Expenses related to clinical studies, preclinical development activities and product manufacturing are based on estimates of the services received and efforts expended pursuant to our contract arrangements. There may be instances in which payments made to our service providers will temporarily exceed the level of services provided and result in a prepayment of the expense. Payments under some of these contracts depend on factors such as, for clinical studies, the successful enrollment of patients, site initiation and the completion of clinical milestones. We make estimates of our accrued expenses as of each balance sheet date based on facts and circumstances known at the time. In accruing service fees, we estimate the time period over which services will be performed and the level of effort to be expended in each period. If the actual timing of the performance of services or the level of effort varies from our estimate, we adjust the accrual or prepaid expense balance accordingly. Historically, our estimated accrued liabilities have materially approximated actual expenses incurred. Leases In January 2019, we adopted Accounting Standards Update (ASU) No. 2016‑02, Leases (Topic 842) We elected the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed us to exclude from our consolidated balance sheets recognition of leases having a term of 12 months or less (short-term leases) and we elected to not separate lease components and non-lease components for our long-term leases. Rent expense for the operating lease is recognized on a straight-line basis over the lease term and is included in operating expenses in our consolidated statements of operations. Prior period amounts continue to be reported in accordance with our historical accounting practices under previous lease guidance, Accounting Standards Codification (ASC) 840, Leases Revenue Recognition We have entered into a research collaboration and option agreement with CSL Behring (CSL). The terms of this arrangement include payments to us for research and development services and potential development milestone payments. Performance of obligations under the agreement began in the second quarter of 2019. We evaluate our agreements under ASC 606, Revenue from Contracts with Customers (Topic 606) and Collaborative Arrangements (Topic 808) . . In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our agreement, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) we satisfy each performance obligation. As part of the accounting for these arrangements, we must develop assumptions that require judgment to determine the stand-alone selling price for each performance obligation identified in the contract. We use key assumptions to determine the stand-alone selling price, which may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success. Research and Development Costs Research and development costs are expensed as incurred. Research and development costs include: salaries and employee-related expenses, including stock-based compensation and benefits for personnel in research and product development functions; costs associated with conducting our preclinical, development and regulatory activities, including fees paid to third-party professional consultants, service providers and our scientific, therapeutic and clinical advisors; costs to acquire, develop and manufacture preclinical study and clinical trial materials; costs incurred under clinical trial agreements with CROs and investigative sites; costs for laboratory supplies; payments related to licensed products and technologies; allocated facilities and information technology costs; and depreciation. Patent Costs Costs related to filing and pursuing patent applications are recorded as general and administrative expense and expensed as incurred since recoverability of such expenditures is uncertain. Stock-Based Compensation Stock-based compensation expense represents the grant date fair value of employee stock option grants recognized as expense over the requisite service period of the awards (usually the vesting period) on a straight-line basis. We estimate fair value of stock option grants using the Black-Scholes option pricing model. We estimate the fair value using assumptions, including the risk-free interest rate, the expected volatility of a peer group of similar companies, the expected term of the awards and the expected dividend yield. These estimates involve inherent uncertainties and the application of management’s judgment. If factors change and different assumptions are used, our stock-based compensation expense could be materially different in the future. We follow Accounting Standards Codification (ASC) Topic 718, Compensation – Stock Compensation Income Taxes We account for income taxes under the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements. Under this method, deferred tax assets and liabilities are determined on the basis of the differences between the financial statements and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. The effect of a change in tax rates on deferred tax assets and liabilities is recognized as income in the period that includes the enactment date. We recognize net deferred tax assets to the extent that we believe these assets are more likely than not to be realized. In making such a determination, we consider all available positive and negative evidence, including future reversals of existing taxable temporary differences, projected future taxable income, tax-planning strategies and results of recent operations. If we determine that we would be able to realize the deferred tax assets in the future in excess of their net recorded amount, we would make an adjustment to the deferred tax asset valuation allowance, which would reduce the provision for income taxes. We record uncertain tax positions on the basis of a two-step process whereby (1) we determine whether it is more likely than not that the tax positions will be sustained on the basis of the technical merits of the position and (2) for those tax positions that meet the more-likely-than-not recognition threshold, we recognize the largest amount of tax benefit that is more than 50% likely to be realized upon ultimate settlement with the related tax authority. We recognize interest and penalties related to unrecognized tax benefits within income tax expense. Any accrued interest and penalties are included within the related tax liability. Net Loss Per Share Basic net loss per share is calculated by dividing the net loss attributable to common stockholders by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents and adjusted for the weighted average number of common shares outstanding that are subject to repurchase. Diluted net loss per share attributable to common stockholders is calculated by dividing the net loss attributable to common stockholders by the weighted average number of common stock equivalents outstanding for the period determined using the treasury-stock method. Dilutive common stock equivalents are comprised of convertible preferred stock, warrants for common stock, options and restricted stock units outstanding under our stock option plan and estimated shares to be purchased under our employee stock purchase plan. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding due to our net loss position. Potentially dilutive securities not included in the calculation of diluted net loss per share because to do so would be anti-dilutive are as follows (in common share equivalents): Years Ended December 31, 2019 2018 2017 Class X Preferred Stock (if-converted to common stock) 587,445 816,851 816,851 Common stock warrants 13,904 477,639 477,639 Common stock options and restricted stock units 363,553 371,823 333,154 Employee stock purchase plan 1,958 1,610 2,220 966,860 1,667,923 1,629,864 The following table summarizes our net loss per share (in thousands, except per share data): Years Ended December 31, 2019 2018 2017 Numerator: Net loss attributable to aTyr Pharma, Inc. $ (23,603 ) $ (34,515 ) $ (48,207 ) Denominator: Weighted average common shares outstanding 3,355,600 2,141,961 1,845,294 Weighted average common shares subject to repurchase — — (261 ) Weighted average common shares outstanding - basic and diluted 3,355,600 2,141,961 1,845,033 Net loss per share - basic and diluted $ (7.03 ) $ (16.11 ) $ (26.13 ) Convertible Preferred Stock We apply the relevant accounting standards to distinguish liabilities from equity when assessing the classification and measurement of preferred stock. Preferred shares subject to mandatory redemptions are considered liabilities and measured at fair value. Conditionally redeemable preferred shares are considered temporary equity. All other preferred shares are considered as stockholders’ equity. None of our outstanding preferred stock has redemption features. Derivative Financial Instruments We do not use derivative instruments to hedge exposures to cash flow, market, or foreign currency risks. We evaluate all of our financial instruments, including warrants, to determine if such instruments are derivatives or contain features that qualify as embedded derivatives. We generally use the Black-Scholes option-pricing model to value the derivative instruments at inception and subsequent valuation dates. The classification of derivative instruments, including whether such instruments should be recorded as liabilities or as equity, is re-assessed at the end of each reporting period. Recent Accounting Pronouncements In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments – Credit Losses (Topic 326), to provide financial statement users with more decision-useful information about the expected credit losses on financial instruments and other commitments to extend credit held by a reporting entity at each reporting date. To achieve this objective, the amendments in ASU No. 2016-13 replace the incurred loss impairment methodology in current GAAP with a methodology that reflects expected credit losses and requires consideration of a broader range of reasonable and supportable information to inform credit loss estimates. ASU No. 2016-13 is effective for fiscal years beginning after December 15, 2020, including periods within those fiscal years. We are currently evaluating the impact of ASU No. 2016-13 and do not expect the adoption of this guidance will have a material impact on our consolidated financial position or results of operations. In June 2018, the FASB issued ASU No. 2018-07, Compensation – Stock Compensation (Topic 718) n entity to apply the requirements of Topic 718 to nonemployee awards except for specific guidance on inputs to an option pricing model and the attribution of cost (that is, the period of time over which share-based payment awards vest and the pattern of cost recognition over that period). The amendments specify that Topic 718 applies to all share-based payment transactions in which a grantor acquires goods or services to be used or consumed in a grantor’s own operations by issuing share-based payment awards. The amendments also clarify that Topic 718 does not apply to share-based payments used to effectively provide (1) inancing to the issuer or (2) awards granted in conjunction with selling goods or services to customers as part of a contract accounted for under Topic 606, Revenue from Contracts with Customers . In July 2018, the FASB issued ASU No. 2018-09, Codification Improvements Amendments to Subtopic 718-40, Compensation–Stock Compensation–Income Taxes, deductions that are taken on the entity’s tax return in a different period from when the event that gives rise to the tax deduction occurs and the uncertainty about whether (1) the entity will receive a tax deduction and (2) the amount of the tax deduction is resolved. Some of the amendments in ASU No. 2018-09 do not require transition guidance and are effective immediately and others have transition guidance with effective dates for annual periods beginning after December 15, 2018 which we adopted on January 1, 2019. T In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808) clarify the interaction between Topic 808 and Topic 606. A collaborative arrangement, as defined by the guidance in Topic 808, is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. Topic 808 does not provide comprehensive recognition or measurement guidance for collaborative arrangements, and the accounting for those arrangements is often based on an analogy to other accounting literature or an accounting policy election. Some entities apply revenue guidance directly or by analogy to all or part of their arrangements, and others apply a different accounting method as an accounting policy. Those accounting differences result in diversity in practice on how entities account for transactions on the basis of their view of the economics of the collaborative arrangement. We early adopted ASU No. 2018-18 in the second quarter of 2019 and the adoption of this guidance did not have a material impact on our consolidated financial position or results of operations. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes (Topic 740), Simplifying the Accounting for Income Taxes

Fair Value Measurements

Fair Value Measurements	12 Months Ended
	Dec. 31, 2019
Fair Value Disclosures [Abstract]
Fair Value Measurements	3. Fair Value Measurements The carrying amounts of cash equivalents, prepaid and other assets, accounts payable and accrued liabilities are considered to be representative of their respective fair values because of the short-term nature of those instruments. Based on the borrowing rates currently available to us for loans with similar terms, which is considered a Level 2 input, we believe that the fair value of our Term Loans approximate its carrying values. Investment securities are recorded at fair value. The accounting guidance defines fair value, establishes a consistent framework for measuring fair value and expands disclosure for each major asset and liability category measured at fair value on either a recurring or nonrecurring basis. Fair value is defined as an exit price, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset or liability. As a basis for considering such assumptions, the accounting guidance establishes a three-tier fair value hierarchy, which prioritizes the inputs used in measuring fair value as follows: Level 1: Observable inputs such as quoted prices in active markets. Level 2: Inputs, other than the quoted prices in active markets that are observable either directly or indirectly. Level 3: Unobservable inputs in which there is little or no market data, which require the reporting entity to develop its own assumptions. Financial assets measured at fair value on a recurring basis consist of investment securities. Investment securities are recorded at fair value, defined as the exit price in the principal market in which we would transact, representing the amount that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants. Level 2 securities are valued using quoted market prices for similar instruments, non-binding market prices that are corroborated by observable market data, or discounted cash flow techniques and include our investments in asset-backed securities, commercial paper, and corporate debt securities. We have no financial liabilities measured at fair value on a recurring basis. None of our non-financial assets and liabilities is recorded at fair value on a non-recurring basis. No transfers between levels have occurred during the periods presented. Assets and liabilities measured at fair value on a recurring basis are as follows (in thousands): Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2019 Assets: Current: Cash equivalents $ 8,248 $ 8,248 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 6,304 — 6,304 — Commercial paper 7,568 — 7,568 — Corporate debt securities 8,062 — 8,062 — Total short-term investments 21,934 — 21,934 — Total assets measured at fair value $ 30,182 $ 8,248 $ 21,934 $ — Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2018 Assets: Current: Cash equivalents $ 16,019 $ 16,019 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 7,773 — 7,773 — Commercial paper 6,144 — 6,144 — Corporate debt securities 12,666 — 12,666 — Total short-term investments 26,583 — 26,583 — Total assets measured at fair value $ 42,602 $ 16,019 $ 26,583 $ — As of December 31, 2019 and 2018, available-for-sale investments are detailed as follows (in thousands): December 31, 2019 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 6,299 $ 5 $ — $ 6,304 Commercial paper 7,568 — — 7,568 Corporate debt securities 8,057 5 — 8,062 $ 21,924 $ 10 $ — $ 21,934 December 31, 2018 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 7,777 $ — $ (4 ) $ 7,773 Commercial paper 6,144 — — 6,144 Corporate debt securities 12,672 — (6 ) 12,666 $ 26,593 $ — $ (10 ) $ 26,583 At each reporting date, we perform an evaluation of impairment to determine if the unrealized losses are other-than-temporary. Factors considered in determining whether a loss is other-than-temporary include the length of time and extent to which fair value has been less than the cost basis, the financial condition of the issuer, and our intent and ability to hold the investment until recovery of its amortized cost basis. As of December 31, 2019, all available-for-sale investments were in a gross unrealized gain position, and had been in such position for less than twelve months.

License Agreement

License Agreement	12 Months Ended
	Dec. 31, 2019
License Agreement [Abstract]
License Agreement	4. License Agreement In March 2019, we entered into a research collaboration and option agreement with CSL for the development of product candidates derived from up to four tRNA synthetases from our preclinical pipeline (CSL Agreement). Under the terms of the CSL Agreement, CSL will fund all research and development activities related to the development of the applicable product candidates for the duration of the collaboration. CSL reimburses us for all research and development activities. The research and development activities will be performed in six phases by both parties. The first phase totaling $0.6 million was funded in May 2019 and future phases will be funded on a quarterly basis. In addition, CSL will pay a total of up to $4.25 million per synthetase program ($17 million if all four synthetase programs advance) in option fees based on achievement of research milestones and CSL’s determination to continue development. As of December 31, 2019, no research milestones had been met. We will grant CSL an option to negotiate licenses for worldwide rights to each investigational new drug (IND) candidate that emerges from this research collaboration. Specific license terms will be negotiated during an exclusivity period following the exercise of each program option. CSL has the right to terminate the research collaboration and option agreement in its entirety or with respect to one or more synthetases upon 45 days notice. Either party has the right to terminate the agreement upon material breach of obligation or insolvency of the other party. We assessed our research collaboration with CSL in accordance with Topic 606 and concluded that CSL is a customer. We identified the following performance obligations under the CSL Agreement: 1) research services; and 2) participation in the Joint Steering Committee. We concluded that the performance obligations are interrelated and do not have a standalone basis. CSL has the right to terminate the research collaboration upon 45 days notice, which is considered to be the legally enforceable contract term. Therefore, during the first phase of research services, we have a 45 day performance obligation and all research services beyond the initial 45 days performance obligation are considered a material right. In addition, each phase of research services represents a separate customer option since CSL must provide written notice of its intent to advance to the next phase. Under the CSL Agreement, CSL is obligated to pay us for the costs incurred by us under the research programs. The payment of $0.6 million for the first phase of the research program received in May 2019 was considered fixed consideration and we will recognize revenue on the payment for the research service performance obligation as the services are performed. We are utilizing a cost-based input method to measure proportional performance and to calculate the corresponding amount of revenue to recognize. We believe this is the best measure of progress because other measures do not reflect how we transfer the performance obligation to our counterparty. In applying the cost-based input methods of revenue recognition, we use actual costs incurred relative to budgeted costs to fulfill the combined performance obligation. These costs consist primarily of third-party contract costs and internal full-time equivalent effort. A cost-based input method of revenue recognition requires us to make estimates of costs to complete the performance obligations. The cumulative effect of revisions to estimated costs to complete the performance obligations will be recorded in the period in which changes are identified and amounts can be reasonably estimated. A significant change in these assumptions and estimates could have a material impact on the timing and amount of revenue recognized in future periods. The option fees based on research milestones under the CSL Agreement are variable consideration. Because they are binary in nature, we will use the “most-likely” method to evaluate whether the milestones should be included. However, the milestones are only payable upon CSL’s decision to proceed to the next research phase for any program, and are therefore subject to CSL’s sole discretion. Accordingly, the milestones are fully constrained and we will not recognize revenue related to these amounts until we have received notification from CSL that they would like to proceed with the next phase of a research program. For the year ended December 31, 2019, we recognized $422,000 as collaboration revenue under the CSL Agreement.

Balance Sheet Details

Balance Sheet Details	12 Months Ended
	Dec. 31, 2019
Balance Sheet Details [Abstract]
Balance Sheet Details	5. Balance Sheet Details Property and equipment consist of the following (in thousands): December 31, 2019 2018 Computer and office equipment $ 543 $ 543 Scientific and laboratory equipment 5,241 5,631 Tenant improvements 1,700 1,703 7,484 7,877 Less accumulated depreciation and amortization (6,214 ) (6,024 ) $ 1,270 $ 1,853 As of December 31, 2019, 2018 and 2017, depreciation expense was $0.6 million, $0.7 million and $0.7 million, respectively. Accrued expenses consist of the following (in thousands): December 31, 2019 2018 Accrued salaries, wages and benefits $ 1,275 $ 1,309 Other accrued expenses (1) 1,101 717 $ 2,376 $ 2,026 (1) Other accrued expenses include expenses for clinical research organizations and contract manufacturing organizations.

Debt, Commitments and Contingen

Debt, Commitments and Contingencies	12 Months Ended
	Dec. 31, 2019
Debt Instruments [Abstract]
Debt, Commitments and Contingencies	6. Debt, Commitments and Contingencies Term Loans In November 2016, we entered into a loan and security agreement and subsequently entered amendments (collectively, the Loan Agreement), for term loans with Silicon Valley Bank (SVB) and Solar Capital Ltd. (Solar), to borrow up to $20.0 million issuable in three separate tranches (the Term Loans), $10.0 million of which was funded in November 2016, $5.0 million of which was funded in June 2017 and $5.0 million of which was funded in December 2017. Under the Loan Agreement, we are obligated to make interest only payments through June 1, 2018, followed by consecutive equal monthly payments of principal and interest in arrears through the maturity date of November 18, 2020. Accordingly, we started paying the Term Loans in June 2018. The Term Loans bear interest at the prime rate, as reported in The Wall Street Journal on the last date of the month preceding the month in which interest will accrue, plus 4.10%. A final payment equal to 8.75% of the funded amounts is payable when the Term Loans become due or upon the prepayment of the respective outstanding balance. We have the option to prepay the outstanding balance of the loan in full, subject to a prepayment fee ranging from 1.0% to 3.0% depending upon when the prepayment occurs, as well as any non-usage fees. The obligations under the Term Loans are secured by liens on our tangible personal property and we agreed to not encumber any of our intellectual property. The Term Loans include a material adverse change clause, which, if invoked, would enable the Lenders to require immediate repayment of the outstanding debt. The material adverse change clause covers a material impairment in the perfection or priority of the Lenders’ lien in the underlying collateral or in the value of such collateral, material adverse change in business operations or condition or material impairment of our prospects for repayment of any portion of the remaining debt obligation. As of December 31, 2019 the carrying value of our Term Loans consisted of $7.3 million principal outstanding, less the debt issuance costs of $0.1 million and the accretion of the final maturity payment of $1.8 million. We intend to pay our Term Loans in full, including the final maturity payment by the fourth quarter of 2020. The debt issuance costs have been recorded as a debt discount, and are being accreted to interest expense over the life of the Term Loans. In connection with the first tranche, we issued warrants to each of SVB and Solar to purchase an aggregate of 3,415 shares of our common stock with an exercise price of $43.93 per share. In connection with the second tranche, we issued warrants to each of SVB and Solar to purchase an aggregate of 1,489 shares of our common stock with an exercise price of $50.37 per share. In connection with the third tranche, we issued warrants to each of SVB and Solar to purchase an aggregate of 1,443 shares of our common stock with an exercise price of $51.98 per share. The warrants are immediately exercisable and have a maximum contractual term of seven years. The aggregate fair value of the warrants was determined to be $0.5 million using the Black-Scholes option pricing model and was recorded as debt discount which are being accreted to interest expense over the life of Term Loans. Facility Lease W e adopted ASU No. 2016-02, utilizing the modified retrospective transition method at the beginning of the first quarter of 2019. We elected the package of practical expedients requiring no reassessment of whether any expired or existing contracts are or contain leases, the lease classification of any expired or existing leases, or initial direct costs for any existing leases. We did not elect the hindsight practical expedient. We also made accounting policy elections not to apply the recognition requirements under ASU No. 2016-02 to any of our short-term leases and to account for each separate lease and associated non-lease components as a single lease component for all of our leases. Under ASU No. 2016-02, we determine if an arrangement is a lease at inception. The adoption of the new lease standard had a material impact on the consolidated balance sheets, but did not have a material impact on the consolidated statements of operations. The impact on the consolidated balance sheet resulted in the recording of a $3.5 million right-of-use asset and a corresponding operating lease liability for the same amount. Our right-of-use assets consist of an operating lease for our facility headquarters. We utilize a discount rate (incremental borrowing rate) of 9.6%. Rent expense for the years ended December 31, 2019, 2018 and 20176 was $1.0 million, $1.0 million and $0.9 million, respectively. A s of December 31, 2019, the weighted average remaining lease term was 3.4 years and the weighted average discount rate was 9.6%. Future minimum payments under the non-cancelable facility lease and reconciliation to the operating lease liability as of December 31, 2019 were as follows (in thousands): Operating Lease 2020 $ 1,002 2021 1,031 2022 1,062 2023 404 Less: Amount representing interest (505 ) Present value of lease payments 2,994 Less: Current portion of operating lease liability (755 ) Long-term operating lease liability $ 2,239 Related Party Transactions Research Agreements and Funding Obligations We provided funding to The Scripps Research Institute (TSRI) pursuant to a research funding and option agreement to conduct certain research activities. We terminated of our research funding and option agreement effective as of November 2018. During the years ended December 31, 2018 and 2017, we recognized expense under the agreement in the amount of $1.7 million and $1.8 million , respectively. member of our board of directors, is a faculty member at TSRI and such payments fund a portion of his research activities conducted at TSRI.

Stockholders' Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2019
Equity [Abstract]
Stockholders' Equity	7. Stockholders’ Equity Common Stock At the Market Offering Program In June 2016, we entered into a sales agreement with Cowen and Company, LLC (Cowen) for at the market offerings (ATM Offering Program), under which we were able to offer and sell shares of our common stock having an aggregate offering price of up to $35.0 million from time to time. In May 2019, we terminated the ATM Offering Program with Cowen. During the year and prior to termination in May 2019, we sold an aggregate of 193,670 shares of common stock at an average price of $7.35 per common share for net proceeds of $1.4 million under the ATM Offering Program with Cowen. In May 2019, we entered into a sales agreement with H.C. Wainwright & Co., LLC (Wainwright) to create an ATM Offering Program under which we may offer and sell shares of our common stock having an aggregate offering price of up to $10.0 million. Wainwright is entitled to a commission at a fixed commission rate equal to 3% of the gross proceeds. During the year ended December 31, 2019, we sold an aggregate of 611,687 shares of common stock at an average price of $5.43 per common share for Private Placement of Common Stock, Convertible Preferred Shares and Common Stock Warrants In August 2017, we completed a private placement of common and preferred stock in which a select group of institutional investors, including Viking Global Opportunities Illiquid Investments Sub-Master, LP (VGO Fund) and other accredited investors, certain of whom are affiliated with our directors and officers (collectively, the Purchasers), purchased preferred stock and common stock. We issued to VGO Fund 126,985 shares of our common stock, at a price of $37.10 per share, 2,285,952 shares of our Class X Convertible Preferred Stock, par value of $0.001 at a price of $13.25 per share, and warrants to purchase up to that number of additional shares of common stock. The remaining Purchasers purchased an aggregate of 292,453 shares of our common stock, at a price of $37.10 per share, and warrants to purchase up to 109,743 additional shares of our common stock. Gross proceeds from the private placement were $45.8 million. The warrants to purchase 463,735 shares of our common stock are exercisable at an exercise price of $64.92 per share, subject to adjustments as provided under the terms of the warrants. The warrants expired on December 31, 2019. Each share of preferred stock is convertible into approximately 0.357 shares of our common stock. In January 2019, the VGO Fund converted 641,991 shares of its preferred stock into 229,283 shares of common stock. Registered Direct Offering In April 2019, we entered into a securities purchase agreement with an institutional investor, The Federated Kaufmann Small Cap Fund . 2014 Stock Plan We adopted a stock option plan in 2007 (the 2007 Plan), which was subsequently amended, restated and renamed in July 2014 (the 2014 Plan) to provide for the incentive stock options, nonstatutory stock options, stock and rights to purchase restricted stock to eligible recipients. Recipients of incentive stock options are eligible to purchase shares of our common stock at an exercise price equal to no less than the estimated fair market value of such stock on the date of grant. The maximum term of options under the 2014 Plan is ten years. Options granted generally vest over four years. Shares underlying any awards under the 2014 Plan that are forfeited, canceled, reacquired by us prior to vesting, satisfied without the issuance of stock or otherwise terminated (other than by exercise) will be added to shares available for issuance under the 2015 Plan. 2015 Stock Plan In April 2015, our board of directors adopted, and our stockholders approved, the 2015 Stock Plan (the 2015 Plan). The 2015 Plan became effective on May 6, 2015 and we ceased granting any new awards under our 2014 Plan. Awards granted under the 2014 Plan prior to our IPO that are forfeited, canceled, reacquired by us prior to vesting satisfied without the issuance of stock or otherwise terminated (other than by exercise) will be added to shares available for issuance under the 2015 Plan. A total of 112,399 shares of our common stock were initially reserved for issuance under the 2015 Plan. In addition, the number of shares reserved and available for issuance under the 2015 Plan automatically increased each January 1, beginning on January 1, 2016 and thereafter until January 1, 2019, by the lesser of (i) 131,428 shares, (ii) 4% of the outstanding number of shares of our common stock on the immediately preceding December 31 or (iii) an amount determined by our board of directors. Pursuant to this provision, 87,368, 85,111 and 67,842 additional shares were reserved for issuance under the 2015 Plan on January 1, 2019, 2018 and 2017, respectively. In March 2019, our board of directors amended the 2015 Plan to increase the number of shares of common stock reserved under the 2015 Plan by 71,428 shares subject to approval by the Company’s stockholders. At our 2019 Annual Meeting of Stockholders, our stockholders approved such amendment. Total shares available for issuance under the 2015 Plan as of January 1, 2020 were 260,999. Shares underlying any awards under the 2015 Plan that are forfeited, canceled, reacquired by us prior to vesting, satisfied without the issuance of stock or otherwise terminated (other than by exercise) will be added to shares available for issuance under the 2015 Plan. The maximum term of options granted under 2015 Plan is ten years. For an initial grant to an employee, 25% of the options generally vest on the first anniversary of the original vesting date, with the balance vesting monthly over the remaining three years. For subsequent grants to an employee, the options generally vest monthly over a four-year term. Inducement Grants In July 2018, we granted a non-qualified option to purchase 14,285 shares of our common stock at an exercise price of $11.41 per share as an inducement award in connection with the hiring of our Chief Financial Officer. Options under the inducement grants vest over a period of four years, with 25% vesting on the one year anniversary of the grant date and the remaining 75% vesting on a monthly basis over three years thereafter, subject to continuous employment. These options were inducement grants issued outside of the 2015 Plan in accordance with Nasdaq Listing Rule 5635(c)(4). In addition, from time to time, we may make inducement grants of stock options to new employees. Employee Stock Purchase Plan In April 2015, our board of directors adopted, and our stockholders approved, our 2015 Employee Stock Purchase Plan (the 2015 ESPP). The 2015 ESPP became effective on May 6, 2015. A total of 16,258 shares of our common stock were initially reserved for issuance under the 2015 ESPP. In addition, the number of shares reserved and available for purchase under the 2015 ESPP automatically increased each January 1, beginning on January 1, 2016 and thereafter until January 1, 2019, by 1% of the outstanding number of shares of our common stock on the immediately preceding December 31 or such lesser number of shares as determined by the administrator of the 2015 ESPP. Pursuant to this provision, 21,842, 21,277 and 16,960 additional shares were reserved for issuance under the 2015 ESPP on January 1, 2019, 2018 and 2017, respectively. As of January 1, 2020, total shares reserved for issuance under the 2015 ESPP were 78,697. Stock-based Compensation Stock Options Stock option activity is summarized as follows: Number of Outstanding Options Weighted Average Exercise Price Weighted Remaining Contractual Term Aggregate Intrinsic Value Outstanding as of December 31, 2018 356,353 $ 62.61 Granted 76,722 $ 7.15 Canceled/forfeited/expired (81,997 ) $ 58.98 Outstanding as of December 31, 2019 351,078 $ 51.34 6.60 $ 910.00 Options vested and expected to vest as of December 31, 2019 351,078 $ 51.34 6.60 $ 910.00 Options exercisable as of December 31, 2019 218,021 $ 67.82 5.51 $ 45.00 The assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants were as follows: Years Ended December 31, 2019 2018 2017 Expected term (in years) 5.51 – 6.07 5.00 – 6.08 5.50 – 6.08 Risk-free interest rate 1.4% – 2.6% 2.3% – 3.0% 1.9% – 2.1% Expected volatility 97.2% – 105.4% 87.9% – 98.4% 99.1% – 124.4% Expected dividend yield 0.0% 0.0% 0.0% The assumptions used in the Black-Scholes option pricing model to determine the fair value of the ESPP offering were as follows: Years Ended December 31, 2019 2018 2017 Expected term (in years) 0.50 0.50 0.50 Risk-free interest rate 1.6% – 2.5% 1.4% – 2.1% 0.6% – 1.0% Expected volatility 99.7% – 141.7% 71.5% – 99.7% 74.5% – 115.2% Expected dividend yield 0.0% 0.0% 0.0% Expected term . The expected term represents the period of time that options are expected to be outstanding. Because we do not have sufficient history of exercise behavior, we determine the expected life assumption using the simplified method, which is an average of the contractual term of the option and its vesting period. Risk-free interest rate. We base the risk-free interest rate assumption on the U.S. Treasury’s rates for U.S. Treasury zero-coupon bonds with maturities similar to those of the expected term of the award being valued. Expected volatility. The expected volatility assumption is based on volatilities of a peer group of similar companies whose share prices are publicly available. The peer group was developed based on companies in the biotechnology industry. Expected dividend yield. We base the expected dividend yield assumption on the fact that we have never paid cash dividends and have no present intention to pay cash dividends. Restricted Stock Units Occasionally, we grant restricted stock units to employees. Restricted stock unit activity is summarized as follows: Number of Outstanding Restricted Stock Units Weighted Average Grant Date Fair Value Balance as of December 31, 2018 15,470 $ 11.91 Granted 5,356 $ 7.24 Released (7,487 ) $ 11.91 Forfeited (864 ) $ 11.90 Balance as of December 31, 2019 12,475 $ 9.90 The allocation of stock-based compensation for all options, including performance options with market condition and restricted stock units is as follows (in thousands): Years Ended December 31, 2019 2018 2017 Research and development $ 354 $ 1,216 $ 1,399 General and administrative 1,429 2,215 $ 5,385 Total stock-based compensation expense $ 1,783 $ 3,431 $ 6,784 The weighted–average grant date fair value per share of stock options granted by us, during the years ended December 31, 2019, 2018 and 2017 was $5.67, $25.76 and $39.95, respectively. The total grant date fair value of restricted stock units vested during the years ended December 31, 2019, 2018 and 2017 was $39,000, $0.2 million and $0.1 million, respectively. The aggregate intrinsic value of stock options exercised during the years ended December 31, 2018 and 2017 was $6,000 and $0.3 million, respectively. We did not have any options exercised during the year ended December 31, 2019. The aggregate intrinsic value of restricted stock units released during the years ended December 31, 2019, 2018 and 2017 was $31,000, $19,000 and $0.1 million. As of December 31, 2019, total unrecognized share-based compensation expense related to unvested stock options and restricted stock units was approximately $2.4 million and $0.1 million, respectively. These unrecognized costs for options and restricted stock units are expected to be recognized ratably over a weighted-average period of approximately 2.3 years and 0.7 years, respectively. Warrants Warrants outstanding for the purchase of common stock as of December 31, 2019 were as follows: Number Exercise Price Expiration Outstanding Per Share Date 144 $ 104.65 March 2021 1,066 $ 281.50 July 2023 6,830 $ 43.93 November 2023 2,978 $ 50.37 June 2024 2,886 $ 51.98 December 2024 13,904 Common Stock Reserved for Future Issuance Common stock reserved for future issuance was as follows: December 31, 2019 Class X Preferred Stock (if-converted to common stock) 587,445 Common stock warrants 13,904 Common stock options and restricted stock units 363,553 Shares available under the 2015 Plan 260,999 Shares available under the 2015 ESPP 78,697 1,304,598

Income Tax

Income Tax	12 Months Ended
	Dec. 31, 2019
Income Tax Disclosure [Abstract]
Income Tax	8. Income Tax Pretax earnings (loss) were generated by both domestic and foreign operations as follows (in thousands): Years Ended December 31, 2019 2018 2017 United States $ (23,315 ) $ (34,021 ) $ (47,712 ) Foreign (448 ) (494 ) (495 ) $ (23,763 ) $ (34,515 ) $ (48,207 ) A reconciliation of the expected statutory federal income tax provision to the actual income tax provision is summarized as follows (in thousands): Years Ended December 31, 2019 2018 2017 Expected income taxes benefit at federal statutory rate $ (4,990 ) $ (7,248 ) $ (16,390 ) State income taxes, net of federal benefit (19 ) (14 ) (13 ) Permanent items and other 750 770 1,311 Research credits (817 ) (1,222 ) (2,286 ) Unrecognized tax benefits 327 489 914 Foreign rate differential 20 22 87 Change in tax rate (49 ) (11 ) (25 ) Tax cuts and Jobs Act — — 27,933 Change in valuation allowance 4,778 7,214 (11,531 ) Income tax (benefit) expense $ — $ — $ — Deferred income taxes are provided for temporary differences in recognizing certain income and expense items for financial and tax reporting purposes. The deferred tax assets consisted primarily of the income tax benefits from net operating loss (NOLs) carryforwards, research and development credits and capitalized research and development expenses, along with other accruals and reserves. Valuation allowances of $71.7 million and $66.9 million as of December 31, 2019 and 2018, respectively, have been recorded to offset deferred tax assets as realization of such assets does not meet the more-likely-than-not threshold under ASC 740, Accounting for Income Taxes Significant components of our deferred tax assets are summarized as follows (in thousands): December 31, 2019 2018 Deferred tax assets: Net operating loss carryforwards $ 38,180 $ 32,997 Capitalized research and development expenses 16,900 17,279 Research credits and other state credits 12,452 11,962 Intangible assets 1,841 2,024 Reserve and accruals 2,310 2,667 Lease liability 631 — Valuation allowance (71,702 ) (66,929 ) Total deferred tax assets $ 612 $ — Deferred tax liabilities: Right of use lease assets (612 ) — Total deferred tax liabilities (612 ) — Net deferred tax assets $ — $ — As of December 31, 2019, we had federal NOLs carryforwards of approximately $163.7 million, with $51.2 million of NOLs generated through December 31, 2018 carrying forward indefinitely and $112.5 million of net NOLs that will begin to expire in 2025. NOLs generated after January 1, 2018 are subject to an 80% limitation in accordance with the Tax Cuts and Jobs Act of 2017. We had state net operating loss carryforwards of approximately $163.3 million, and foreign net operating loss carryforwards of $8.0 million. The state net operating losses will begin to expire in 2021. The foreign net operating losses carry over indefinitely. As of December 31, 2019, we had federal and state research and development credit carryforwards of approximately $5.0 million and $4.1 million, respectively, which begin to expire in 2026 for federal purposes and carry over indefinitely for state purposes. We had $12.5 million of federal Orphan Drug Credits as of December 31, 2019, which will begin to expire in 2035. Utilization of the domestic NOLs and research and development credit carryforwards may be subject to a substantial annual limitation due to ownership change limitations that may have occurred or that could occur in the future, as required by Section 382 and 383 of the Internal Revenue Code of 1986, as amended (the Code), as well as similar state and foreign provisions. These ownership changes may limit the amount of NOLs and research and development credit carryforwards that can be utilized annually to offset future taxable income and tax, respectively. In general, an “ownership change” as defined by Section 382 of the Code results from a transaction or series of transactions over a three-year period resulting in an ownership change of more than 50 percentage points of the outstanding stock of a company by certain stockholders. Since the Company’s formation, we raised capital through the issuance of capital stock on several occasions which on its own or combined with the purchasing stockholders’ subsequent disposition of those shares, has resulted in such an ownership change, and could result in an ownership change in the future. Upon the occurrence of an ownership change under Section 382 as outlined above, utilization of the NOLs and research and development credit carryforwards become subject to an annual limitation under Section 382 of the Code, which is determined by first multiplying the value of our stock at the time of the ownership change by the applicable long-term, tax-exempt rate, which could be subject to additional adjustments. Any limitation may result in expiration of a portion of the NOLs or research and development credit carryforwards before utilization. We completed analyses through December 31, 2017, and are in the process of analyzing the impact to our NOLs and research and development tax credit carryforwards. During 2019 and 2018, we decided to postpone completing another Section 382 study until we start utilizing our NOLs. Due to the existence of the valuation allowance, any impact to the NOLs and research and development tax credit carryforwards from Section 382 analysis will be offset by a corresponding adjustment to valuation allowance, resulting in no tax provision impact. Ownership changes that may have occurred subsequent to December 31, 2017, and future ownership changes, including any ownership change resulting from this offering, may further limit our ability to utilize its remaining tax attributes. We recognize a tax benefit from an uncertain tax position when it is more likely than not that the position will be sustained upon examination, including resolutions of any related appeals or litigation processes, based on the technical merits. Income tax positions must meet a more-likely-than-not recognition threshold to be recognized. Our practice is to recognize interest and penalties related to income tax matters in income tax expense. We had no accrual for interest and penalties on our balance sheet and had not recognized interest or penalties in the consolidated statements of operations for the years ended December 31, 2019, 2018 and 2017. Due to the existence of the valuation allowance, future changes in unrecognized tax benefits will not impact our effective tax rate. Uncertain tax positions are evaluated based upon the facts and circumstances that exist at each reporting period. Subsequent changes in judgment based upon new information may lead to changes in recognition, derecognition, and measurement. Adjustments may result, for example, upon resolution of an issue with the taxing authorities, or expiration of a statute of limitations barring an assessment for an issue. The activity related to our unrecognized tax benefits is summarized as follows (in thousands): December 31, 2019 2018 2017 Balance as of beginning of year $ 19,643 $ 16,558 $ 13,000 Increase (decrease) related to prior year tax positions — 2 (189 ) Increase related to current year tax positions 1,659 3,083 3,747 Balance as of end of year $ 21,302 $ 19,643 $ 16,558 We do not anticipate that the amount of unrecognized tax benefits as of December 31, 2019 will change within the next twelve months. We are subject to taxation in the United States, Hong Kong and state jurisdictions. Our tax years from inception are subject to examination by the United States, Hong Kong and California authorities due to carry forward of unutilized NOLs and research and development credits.

Employee Benefits

Employee Benefits	12 Months Ended
	Dec. 31, 2019
Compensation And Retirement Disclosure [Abstract]
Employee Benefits	9. Employee Benefits 401(k) Plan We maintain a defined contribution 401(k) plan available to eligible employees. Employee contributions are voluntary and are determined on an individual basis, limited to the maximum amount allowable under federal tax regulations. In April 2015, our Board of Directors approved a policy, beginning on June 1, 2015, to match employee contributions equal to 50% of the participant’s contribution of up to a maximum of 6% of the participant’s annual salary. We made discretionary contributions totaling $0.2 million during each of the years ended December 31, 2019, 2018 and 2017, respectively.

Quarterly Financial Data (Unaud

Quarterly Financial Data (Unaudited)	12 Months Ended
	Dec. 31, 2019
Quarterly Financial Data [Abstract]
Quarterly Financial Data (Unaudited)	10. Quarterly Financial Data (Unaudited) The following financial information reflects all normal recurring adjustments, which are, in our opinion, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2019 and 2018 are as follows (in thousands, except per share data): For the quarters ended March 31 June 30 September 30 December 31 2019: Operating expenses $ 5,877 $ 5,735 $ 5,682 $ 6,106 Net loss attributable to aTyr Pharma, Inc. (6,137 ) (5,848 ) (5,645 ) (5,973 ) Basic and diluted net loss per share $ (2.54 ) $ (1.80 ) $ (1.47 ) (1.54 ) 2018: Operating expenses $ 10,220 $ 9,960 $ 6,677 $ 5,963 Net loss attributable to aTyr Pharma, Inc. (10,667 ) (10,412 ) (7,114 ) (6,322 ) Basic and diluted net loss per share $ (5.01 ) $ (4.88 ) $ (3.33 ) (2.92 ) Net loss per share is computed independently for each of the quarters presented. Therefore, the sum of the quarterly per-share calculations will not necessarily equal the annual per share calculation.

Subsequent Events

Subsequent Events	12 Months Ended
	Dec. 31, 2019
Subsequent Events [Abstract]
Subsequent Events	11. Subsequent Events In January 2020, we entered into a license with Kyorin Pharmaceutical Co., Ltd. (Kyorin) for the development and commercialization of ATYR1923 for ILDs in Japan. Under the collaboration and license agreement with Kyorin (the Kyorin Agreement), Kyorin received an exclusive right to develop and commercialize ATYR1923 in Japan for all forms of ILDs. We received an $8.0 million upfront payment and we are eligible to receive an additional $167.0 million in the aggregate upon achievement of certain development, regulatory and sales milestones, as well as tiered royalties ranging from the mid-single digits to mid-teens on net sales in Japan. Under the terms of the Kyorin Agreement, Kyorin will fund all research, development, regulatory, marketing and commercialization activities in Japan, as well as support our global development efforts for ATYR1923. In January 2020, the VGO Fund converted 1,142,478 shares of its Preferred Shares into 408,247 shares of common stock and in February 2020, converted 501,483 shares of its Preferred Shares into 179,197 shares of common stock. As of February 2020, following the conversion, VGO Fund owned 6.7% of our common stock. In February 2020, we completed an underwritten follow-on public offering of 4,235,294 shares of our common stock at a price to the public of $4.25 per share. In March 2020, the underwriters fully exercised their over-allotment option for the issuance of an additional 635,294 shares of common stock. The total gross proceeds from the underwritten follow-on public offering, including the over-allotment, was approximately $20.7 million, before deducting underwriting discounts, commissions and offering expenses payable by us. We anticipate using the net proceeds from the offering for general corporate purposes, including clinical trial expenses, research and development expenses, manufacturing expenses, and general administrative expenses. In March 2020, Pangu, together with the Hong Kong University of Science and Technology (HKUST), was awarded a grant of approximately $750,000 to build a high-throughput platform for the development of bi-specific antibodies. The two-year project is being funded by the Hong Kong Government’s Innovation and Technology Commission (ITC) under the Partnership Research Program. The grant will be funded by ITC for approximately 50% of the total estimated project cost, with aTyr contributing the remaining 50%.

Summary of Significant Accoun_2

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Organization and Business	Organization and Business We were incorporated in the state of Delaware on September 8, 2005. We are focused on the discovery and development of innovative medicines based on novel immunological pathways.
Principles of Consolidation	Principles of Consolidation Our consolidated financial statements include our accounts and our 98% majority-owned subsidiary in Hong Kong, Pangu BioPharma Limited (Pangu BioPharma). All intercompany transactions and balances are eliminated in consolidation.
Reverse Stock Split	Reverse Stock Split In June 2019, we filed a Certificate of Amendment to our Restated Certificate of Incorporation with the Secretary of State of the State of Delaware to effect a 1-for-14 reverse stock split of our issued and outstanding common stock. The reverse stock split became effective at 5:00 p.m. Eastern Time on June 28, 2019 and our common stock began trading on a split-adjusted basis on The Nasdaq Capital Market on July 1, 2019. Our consolidated financial statements and these notes give retrospective effect to the reverse stock split for all periods presented. All issued and outstanding common stock, options and warrants exercisable for common stock, restricted stock units, preferred stock conversions to common stock and per share amounts contained in our consolidated financial statements have been retrospectively adjusted.
Liquidity and Financial Condition	Liquidity and Financial Condition We have incurred losses and negative cash flows from operations since our inception. As of December 31, 2019, we had an accumulated deficit of $322.3 million and we expect to continue to incur net losses for the foreseeable future. As of December 31, 2019, our cash, cash equivalents and available-for-sale investments were $31.1 million. Since that time, we received $8.0 million related to the Kyorin Agreement and approximately $20.7 million in gross proceeds from our underwritten follow-on public offering of common stock, before deducting underwriting discounts, commissions and offering expenses payable by us. We believe that our current cash, cash equivalents and available-for-sale investments, will be sufficient to meet our anticipated cash requirements for a period of at least one year from the date of this Annual Report. We do not expect to generate any revenues from product sales unless and until we successfully complete development and obtain regulatory approval for one or more of our product candidates, which we expect will take a number of years at a minimum. If we obtain regulatory approval for any of our product candidates, we expect to incur significant commercialization expenses related to product sales, marketing, manufacturing and distribution. Accordingly, we will need to raise substantial additional capital to fund our operations. The amount and timing of our future funding requirements will depend on many factors, including the pace and results of our preclinical and clinical development efforts and the timing and nature of the regulatory approval process for our product candidates. We anticipate that we will seek to fund our operations through equity offerings, grant funding, collaborations, strategic partnerships and/or licensing arrangements, and when we are closer to commercialization of our product candidates potentially through debt financings. However, we may be unable to raise additional capital or enter into such arrangements when needed on favorable terms or at all. Our failure to raise capital or enter into such arrangements when needed would have a negative impact on our financial condition and ability to develop our product candidates. In May 2018, we implemented a corporate restructuring and program prioritization plan (Restructuring Plan) to streamline our operations and concentrate development efforts on the advancement of our therapeutic candidate, ATYR1923. In connection with the Restructuring Plan, we reduced our workforce by approximately 30% to 42 full-time employees. We completed the workforce reduction in June 2018.
Use of Estimates	Use of Estimates Our consolidated financial statements are prepared in accordance with generally accepted accounting principles (GAAP). The preparation of our consolidated financial statements requires us to make estimates and assumptions that impact the reported amounts of assets, liabilities and expenses and the disclosure of liabilities in our consolidated financial statements and accompanying notes. The most significant estimates in our consolidated financial statements relate to the fair value of equity issuances and awards, and clinical trial and research and development expenses. Although these estimates are based on our knowledge of current events and actions we may undertake in the future, actual results may ultimately differ materially from these estimates and assumptions.
Segment Reporting	Segment Reporting Operating segments are identified as components of an enterprise about which separate discrete financial information is available for evaluation by the chief operating decision-maker in making decisions regarding resource allocation and assessing performance. We view our operations and manage our business in one operating segment.
Reclassifications	Reclassifications Certain reclassifications have been made to prior year amounts to conform to the current year presentation. The reclassifications were not material to the consolidated financial statements.
Cash and Cash Equivalents	Cash and Cash Equivalents Cash and cash equivalents consist primarily of readily available checking, money market accounts and money market funds. We consider all highly liquid investments that mature in three months or less when purchased to be cash equivalents.
Investment Securities	Investment Securities Investment securities primarily consist of investment grade corporate debt securities, asset-backed securities, commercial paper and United States Treasury securities. We classify all investment securities as available-for-sale. Investment securities are carried at fair value, with the unrealized gains and losses, if any, reported as a component of other comprehensive income (loss) in stockholders’ equity until realized. Realized gains and losses from the sale of investment securities, if any, are determined on a specific identification basis. A decline in the market value of any investment security below cost that is determined to be other than temporary will result in an impairment charge to earnings and a new cost basis for the security is established. No such impairment charges were recorded for any period presented. Premiums and discounts are amortized or accreted over the life of the related security as an adjustment to yield using the straight-line method and are included in interest income. Interest income is recognized when earned. As of December 31, 2019, we held an aggregate total of $21.9 million of investment securities which consisted of corporate debt securities, asset-backed securities, and commercial paper all of which will mature in less than one year, and there was an unrealized gain of $8,500 between the amortized cost and fair value of these investment securities. As of December 31, 2018, we held $26.6 million of corporate debt securities, asset-backed securities and United States Treasury securities, all of which mature in less than one year, and there was an unrealized loss of $10,000 between the amortized cost and fair value of these investment securities.
Concentration of Credit Risk	Concentration of Credit Risk Financial instruments that potentially subject us to significant concentration of credit risk consist primarily of cash, cash equivalents and investment securities. We have established guidelines regarding diversification of investments and their maturities, which are designed to maintain principal and maximize liquidity. We maintain deposits in federally insured financial institutions in excess of federally insured limits. We have not experienced any losses in such accounts and we believe that we are not exposed to significant credit risk due to the financial position of the depository institutions in which those deposits are held.
Property and Equipment	Property and Equipment Property and equipment are stated at cost and depreciated on a straight-line basis over the estimated useful life of the related assets (generally three to seven years). Leasehold improvements are stated at cost and amortized on a straight-line basis over the lesser of the remaining term of the related lease or the estimated useful life of the leasehold improvements. Repairs and maintenance costs are charged to expense as incurred .
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Long-lived assets consist primarily of property and equipment. An impairment loss is recorded if and when events and circumstances indicate that assets might be impaired and the undiscounted cash flows estimated to be generated by those assets are less than the carrying amount of those assets. While our current and historical operating losses are indicators of impairment, we believe that future cash flows to be received support the carrying value of our long-lived assets and, accordingly, have not recognized any impairment losses since inception.
Accrued Expenses	Accrued Expenses Expenses related to clinical studies, preclinical development activities and product manufacturing are based on estimates of the services received and efforts expended pursuant to our contract arrangements. There may be instances in which payments made to our service providers will temporarily exceed the level of services provided and result in a prepayment of the expense. Payments under some of these contracts depend on factors such as, for clinical studies, the successful enrollment of patients, site initiation and the completion of clinical milestones. We make estimates of our accrued expenses as of each balance sheet date based on facts and circumstances known at the time. In accruing service fees, we estimate the time period over which services will be performed and the level of effort to be expended in each period. If the actual timing of the performance of services or the level of effort varies from our estimate, we adjust the accrual or prepaid expense balance accordingly. Historically, our estimated accrued liabilities have materially approximated actual expenses incurred.
Leases	Leases In January 2019, we adopted Accounting Standards Update (ASU) No. 2016‑02, Leases (Topic 842) We elected the package of practical expedients permitted under the transition guidance within the new standard, which among other things, allowed us to exclude from our consolidated balance sheets recognition of leases having a term of 12 months or less (short-term leases) and we elected to not separate lease components and non-lease components for our long-term leases. Rent expense for the operating lease is recognized on a straight-line basis over the lease term and is included in operating expenses in our consolidated statements of operations. Prior period amounts continue to be reported in accordance with our historical accounting practices under previous lease guidance, Accounting Standards Codification (ASC) 840, Leases
Revenue Recognition	Revenue Recognition We have entered into a research collaboration and option agreement with CSL Behring (CSL). The terms of this arrangement include payments to us for research and development services and potential development milestone payments. Performance of obligations under the agreement began in the second quarter of 2019. We evaluate our agreements under ASC 606, Revenue from Contracts with Customers (Topic 606) and Collaborative Arrangements (Topic 808) . . In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our agreement, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations; and (v) recognition of revenue when (or as) we satisfy each performance obligation. As part of the accounting for these arrangements, we must develop assumptions that require judgment to determine the stand-alone selling price for each performance obligation identified in the contract. We use key assumptions to determine the stand-alone selling price, which may include forecasted revenues, development timelines, reimbursement rates for personnel costs, discount rates and probabilities of technical and regulatory success.
Research and Development Costs	Research and Development Costs Research and development costs are expensed as incurred. Research and development costs include: salaries and employee-related expenses, including stock-based compensation and benefits for personnel in research and product development functions; costs associated with conducting our preclinical, development and regulatory activities, including fees paid to third-party professional consultants, service providers and our scientific, therapeutic and clinical advisors; costs to acquire, develop and manufacture preclinical study and clinical trial materials; costs incurred under clinical trial agreements with CROs and investigative sites; costs for laboratory supplies; payments related to licensed products and technologies; allocated facilities and information technology costs; and depreciation.
Patent Costs	Patent Costs Costs related to filing and pursuing patent applications are recorded as general and administrative expense and expensed as incurred since recoverability of such expenditures is uncertain.
Stock-Based Compensation	Stock-Based Compensation Stock-based compensation expense represents the grant date fair value of employee stock option grants recognized as expense over the requisite service period of the awards (usually the vesting period) on a straight-line basis. We estimate fair value of stock option grants using the Black-Scholes option pricing model. We estimate the fair value using assumptions, including the risk-free interest rate, the expected volatility of a peer group of similar companies, the expected term of the awards and the expected dividend yield. These estimates involve inherent uncertainties and the application of management’s judgment. If factors change and different assumptions are used, our stock-based compensation expense could be materially different in the future. We follow Accounting Standards Codification (ASC) Topic 718, Compensation – Stock Compensation
Income Taxes	Income Taxes We account for income taxes under the asset and liability method, which requires the recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements. Under this method, deferred tax assets and liabilities are determined on the basis of the differences between the financial statements and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. The effect of a change in tax rates on deferred tax assets and liabilities is recognized as income in the period that includes the enactment date. We recognize net deferred tax assets to the extent that we believe these assets are more likely than not to be realized. In making such a determination, we consider all available positive and negative evidence, including future reversals of existing taxable temporary differences, projected future taxable income, tax-planning strategies and results of recent operations. If we determine that we would be able to realize the deferred tax assets in the future in excess of their net recorded amount, we would make an adjustment to the deferred tax asset valuation allowance, which would reduce the provision for income taxes. We record uncertain tax positions on the basis of a two-step process whereby (1) we determine whether it is more likely than not that the tax positions will be sustained on the basis of the technical merits of the position and (2) for those tax positions that meet the more-likely-than-not recognition threshold, we recognize the largest amount of tax benefit that is more than 50% likely to be realized upon ultimate settlement with the related tax authority. We recognize interest and penalties related to unrecognized tax benefits within income tax expense. Any accrued interest and penalties are included within the related tax liability.
Net Loss Per Share	Net Loss Per Share Basic net loss per share is calculated by dividing the net loss attributable to common stockholders by the weighted average number of common shares outstanding for the period, without consideration for common stock equivalents and adjusted for the weighted average number of common shares outstanding that are subject to repurchase. Diluted net loss per share attributable to common stockholders is calculated by dividing the net loss attributable to common stockholders by the weighted average number of common stock equivalents outstanding for the period determined using the treasury-stock method. Dilutive common stock equivalents are comprised of convertible preferred stock, warrants for common stock, options and restricted stock units outstanding under our stock option plan and estimated shares to be purchased under our employee stock purchase plan. For all periods presented, there is no difference in the number of shares used to calculate basic and diluted shares outstanding due to our net loss position. Potentially dilutive securities not included in the calculation of diluted net loss per share because to do so would be anti-dilutive are as follows (in common share equivalents): Years Ended December 31, 2019 2018 2017 Class X Preferred Stock (if-converted to common stock) 587,445 816,851 816,851 Common stock warrants 13,904 477,639 477,639 Common stock options and restricted stock units 363,553 371,823 333,154 Employee stock purchase plan 1,958 1,610 2,220 966,860 1,667,923 1,629,864 The following table summarizes our net loss per share (in thousands, except per share data): Years Ended December 31, 2019 2018 2017 Numerator: Net loss attributable to aTyr Pharma, Inc. $ (23,603 ) $ (34,515 ) $ (48,207 ) Denominator: Weighted average common shares outstanding 3,355,600 2,141,961 1,845,294 Weighted average common shares subject to repurchase — — (261 ) Weighted average common shares outstanding - basic and diluted 3,355,600 2,141,961 1,845,033 Net loss per share - basic and diluted $ (7.03 ) $ (16.11 ) $ (26.13 )
Convertible Preferred Stock	Convertible Preferred Stock We apply the relevant accounting standards to distinguish liabilities from equity when assessing the classification and measurement of preferred stock. Preferred shares subject to mandatory redemptions are considered liabilities and measured at fair value. Conditionally redeemable preferred shares are considered temporary equity. All other preferred shares are considered as stockholders’ equity. None of our outstanding preferred stock has redemption features.
Derivative Financial Instruments	Derivative Financial Instruments We do not use derivative instruments to hedge exposures to cash flow, market, or foreign currency risks. We evaluate all of our financial instruments, including warrants, to determine if such instruments are derivatives or contain features that qualify as embedded derivatives. We generally use the Black-Scholes option-pricing model to value the derivative instruments at inception and subsequent valuation dates. The classification of derivative instruments, including whether such instruments should be recorded as liabilities or as equity, is re-assessed at the end of each reporting period.
Recent Accounting Pronouncements	Recent Accounting Pronouncements In February 2016, the FASB issued ASU No. 2016-02, Leases (Topic 842) In June 2016, the FASB issued ASU No. 2016-13, Financial Instruments – Credit Losses (Topic 326), to provide financial statement users with more decision-useful information about the expected credit losses on financial instruments and other commitments to extend credit held by a reporting entity at each reporting date. To achieve this objective, the amendments in ASU No. 2016-13 replace the incurred loss impairment methodology in current GAAP with a methodology that reflects expected credit losses and requires consideration of a broader range of reasonable and supportable information to inform credit loss estimates. ASU No. 2016-13 is effective for fiscal years beginning after December 15, 2020, including periods within those fiscal years. We are currently evaluating the impact of ASU No. 2016-13 and do not expect the adoption of this guidance will have a material impact on our consolidated financial position or results of operations. In June 2018, the FASB issued ASU No. 2018-07, Compensation – Stock Compensation (Topic 718) n entity to apply the requirements of Topic 718 to nonemployee awards except for specific guidance on inputs to an option pricing model and the attribution of cost (that is, the period of time over which share-based payment awards vest and the pattern of cost recognition over that period). The amendments specify that Topic 718 applies to all share-based payment transactions in which a grantor acquires goods or services to be used or consumed in a grantor’s own operations by issuing share-based payment awards. The amendments also clarify that Topic 718 does not apply to share-based payments used to effectively provide (1) inancing to the issuer or (2) awards granted in conjunction with selling goods or services to customers as part of a contract accounted for under Topic 606, Revenue from Contracts with Customers . In July 2018, the FASB issued ASU No. 2018-09, Codification Improvements Amendments to Subtopic 718-40, Compensation–Stock Compensation–Income Taxes, deductions that are taken on the entity’s tax return in a different period from when the event that gives rise to the tax deduction occurs and the uncertainty about whether (1) the entity will receive a tax deduction and (2) the amount of the tax deduction is resolved. Some of the amendments in ASU No. 2018-09 do not require transition guidance and are effective immediately and others have transition guidance with effective dates for annual periods beginning after December 15, 2018 which we adopted on January 1, 2019. T In November 2018, the FASB issued ASU No. 2018-18, Collaborative Arrangements (Topic 808) clarify the interaction between Topic 808 and Topic 606. A collaborative arrangement, as defined by the guidance in Topic 808, is a contractual arrangement under which two or more parties actively participate in a joint operating activity and are exposed to significant risks and rewards that depend on the activity’s commercial success. Topic 808 does not provide comprehensive recognition or measurement guidance for collaborative arrangements, and the accounting for those arrangements is often based on an analogy to other accounting literature or an accounting policy election. Some entities apply revenue guidance directly or by analogy to all or part of their arrangements, and others apply a different accounting method as an accounting policy. Those accounting differences result in diversity in practice on how entities account for transactions on the basis of their view of the economics of the collaborative arrangement. We early adopted ASU No. 2018-18 in the second quarter of 2019 and the adoption of this guidance did not have a material impact on our consolidated financial position or results of operations. In December 2019, the FASB issued ASU No. 2019-12, Income Taxes (Topic 740), Simplifying the Accounting for Income Taxes

Summary of Significant Accoun_3

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2019
Accounting Policies [Abstract]
Schedule of Potentially Dilutive Securities Not Included in Calculation of Diluted Net Loss Per Share	Potentially dilutive securities not included in the calculation of diluted net loss per share because to do so would be anti-dilutive are as follows (in common share equivalents): Years Ended December 31, 2019 2018 2017 Class X Preferred Stock (if-converted to common stock) 587,445 816,851 816,851 Common stock warrants 13,904 477,639 477,639 Common stock options and restricted stock units 363,553 371,823 333,154 Employee stock purchase plan 1,958 1,610 2,220 966,860 1,667,923 1,629,864
Summary of Net Loss Per Share	The following table summarizes our net loss per share (in thousands, except per share data): Years Ended December 31, 2019 2018 2017 Numerator: Net loss attributable to aTyr Pharma, Inc. $ (23,603 ) $ (34,515 ) $ (48,207 ) Denominator: Weighted average common shares outstanding 3,355,600 2,141,961 1,845,294 Weighted average common shares subject to repurchase — — (261 ) Weighted average common shares outstanding - basic and diluted 3,355,600 2,141,961 1,845,033 Net loss per share - basic and diluted $ (7.03 ) $ (16.11 ) $ (26.13 )

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	12 Months Ended
	Dec. 31, 2019
Fair Value Disclosures [Abstract]
Schedule of Assets and Liabilities Measured at Fair Value on Recurring Basis	Assets and liabilities measured at fair value on a recurring basis are as follows (in thousands): Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2019 Assets: Current: Cash equivalents $ 8,248 $ 8,248 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 6,304 — 6,304 — Commercial paper 7,568 — 7,568 — Corporate debt securities 8,062 — 8,062 — Total short-term investments 21,934 — 21,934 — Total assets measured at fair value $ 30,182 $ 8,248 $ 21,934 $ — Fair Value Measurements Using Total Quoted Active for Assets (Level 1) Significant Other Observable Inputs (Level 2) Significant Unobservable Inputs (Level 3) As of December 31, 2018 Assets: Current: Cash equivalents $ 16,019 $ 16,019 $ — $ — Available-for-sale investments, short-term: Asset-backed securities 7,773 — 7,773 — Commercial paper 6,144 — 6,144 — Corporate debt securities 12,666 — 12,666 — Total short-term investments 26,583 — 26,583 — Total assets measured at fair value $ 42,602 $ 16,019 $ 26,583 $ —
Schedule of Available-for-sale Investments	As of December 31, 2019 and 2018, available-for-sale investments are detailed as follows (in thousands): December 31, 2019 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 6,299 $ 5 $ — $ 6,304 Commercial paper 7,568 — — 7,568 Corporate debt securities 8,057 5 — 8,062 $ 21,924 $ 10 $ — $ 21,934 December 31, 2018 Gross Amortized Cost Gross Unrealized Gains Gross Unrealized Losses Market Value Available-for-sale investments, short-term: Asset-backed securities $ 7,777 $ — $ (4 ) $ 7,773 Commercial paper 6,144 — — 6,144 Corporate debt securities 12,672 — (6 ) 12,666 $ 26,593 $ — $ (10 ) $ 26,583

Balance Sheet Details (Tables)

Balance Sheet Details (Tables)	12 Months Ended
	Dec. 31, 2019
Balance Sheet Details [Abstract]
Summary of Property and Equipment	Property and equipment consist of the following (in thousands): December 31, 2019 2018 Computer and office equipment $ 543 $ 543 Scientific and laboratory equipment 5,241 5,631 Tenant improvements 1,700 1,703 7,484 7,877 Less accumulated depreciation and amortization (6,214 ) (6,024 ) $ 1,270 $ 1,853
Summary of Accrued Expenses	Accrued expenses consist of the following (in thousands): December 31, 2019 2018 Accrued salaries, wages and benefits $ 1,275 $ 1,309 Other accrued expenses (1) 1,101 717 $ 2,376 $ 2,026 (1) Other accrued expenses include expenses for clinical research organizations and contract manufacturing organizations.

Debt, Commitments and Conting_2

Debt, Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2019
Debt Instruments [Abstract]
Schedule of Future Minimum Payments under Non-cancelable Operating Lease and Reconciliation to Operating Lease Liability	Future minimum payments under the non-cancelable facility lease and reconciliation to the operating lease liability as of December 31, 2019 were as follows (in thousands): Operating Lease 2020 $ 1,002 2021 1,031 2022 1,062 2023 404 Less: Amount representing interest (505 ) Present value of lease payments 2,994 Less: Current portion of operating lease liability (755 ) Long-term operating lease liability $ 2,239

Stockholders' Equity (Tables)

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2019
Summary of Stock Option Activity	Stock option activity is summarized as follows: Number of Outstanding Options Weighted Average Exercise Price Weighted Remaining Contractual Term Aggregate Intrinsic Value Outstanding as of December 31, 2018 356,353 $ 62.61 Granted 76,722 $ 7.15 Canceled/forfeited/expired (81,997 ) $ 58.98 Outstanding as of December 31, 2019 351,078 $ 51.34 6.60 $ 910.00 Options vested and expected to vest as of December 31, 2019 351,078 $ 51.34 6.60 $ 910.00 Options exercisable as of December 31, 2019 218,021 $ 67.82 5.51 $ 45.00
Summary of Assumptions Used to Determine Fair Value of Employee Stock Purchase Plan	The assumptions used in the Black-Scholes option pricing model to determine the fair value of the ESPP offering were as follows: Years Ended December 31, 2019 2018 2017 Expected term (in years) 0.50 0.50 0.50 Risk-free interest rate 1.6% – 2.5% 1.4% – 2.1% 0.6% – 1.0% Expected volatility 99.7% – 141.7% 71.5% – 99.7% 74.5% – 115.2% Expected dividend yield 0.0% 0.0% 0.0%
Schedule of Restricted Stock Units Activity	Occasionally, we grant restricted stock units to employees. Restricted stock unit activity is summarized as follows: Number of Outstanding Restricted Stock Units Weighted Average Grant Date Fair Value Balance as of December 31, 2018 15,470 $ 11.91 Granted 5,356 $ 7.24 Released (7,487 ) $ 11.91 Forfeited (864 ) $ 11.90 Balance as of December 31, 2019 12,475 $ 9.90
Schedule of Allocation of Stock-Based Compensation for All Options Including Performance Options with Market Condition and Restricted Stock Units	The allocation of stock-based compensation for all options, including performance options with market condition and restricted stock units is as follows (in thousands): Years Ended December 31, 2019 2018 2017 Research and development $ 354 $ 1,216 $ 1,399 General and administrative 1,429 2,215 $ 5,385 Total stock-based compensation expense $ 1,783 $ 3,431 $ 6,784
Summary of Warrants Outstanding	Warrants outstanding for the purchase of common stock as of December 31, 2019 were as follows: Number Exercise Price Expiration Outstanding Per Share Date 144 $ 104.65 March 2021 1,066 $ 281.50 July 2023 6,830 $ 43.93 November 2023 2,978 $ 50.37 June 2024 2,886 $ 51.98 December 2024 13,904
Summary of Common Stock Reserved for Future Issuance	Common stock reserved for future issuance was as follows: December 31, 2019 Class X Preferred Stock (if-converted to common stock) 587,445 Common stock warrants 13,904 Common stock options and restricted stock units 363,553 Shares available under the 2015 Plan 260,999 Shares available under the 2015 ESPP 78,697 1,304,598
Employee Stock Option [Member]
Summary of Assumptions Used to Determine Fair Value of Employee Stock Option Grants and Performance Options with Market Condition	The assumptions used in the Black-Scholes option pricing model to determine the fair value of the employee stock option grants were as follows: Years Ended December 31, 2019 2018 2017 Expected term (in years) 5.51 – 6.07 5.00 – 6.08 5.50 – 6.08 Risk-free interest rate 1.4% – 2.6% 2.3% – 3.0% 1.9% – 2.1% Expected volatility 97.2% – 105.4% 87.9% – 98.4% 99.1% – 124.4% Expected dividend yield 0.0% 0.0% 0.0%

Income Tax (Tables)

Income Tax (Tables)	12 Months Ended
	Dec. 31, 2019
Income Tax Disclosure [Abstract]
Schedule of Pretax Earnings (Loss) for Domestic and Foreign Operations	Pretax earnings (loss) were generated by both domestic and foreign operations as follows (in thousands): Years Ended December 31, 2019 2018 2017 United States $ (23,315 ) $ (34,021 ) $ (47,712 ) Foreign (448 ) (494 ) (495 ) $ (23,763 ) $ (34,515 ) $ (48,207 )
Schedule of Reconciliations of the Expected Statutory Federal Income Tax	A reconciliation of the expected statutory federal income tax provision to the actual income tax provision is summarized as follows (in thousands): Years Ended December 31, 2019 2018 2017 Expected income taxes benefit at federal statutory rate $ (4,990 ) $ (7,248 ) $ (16,390 ) State income taxes, net of federal benefit (19 ) (14 ) (13 ) Permanent items and other 750 770 1,311 Research credits (817 ) (1,222 ) (2,286 ) Unrecognized tax benefits 327 489 914 Foreign rate differential 20 22 87 Change in tax rate (49 ) (11 ) (25 ) Tax cuts and Jobs Act — — 27,933 Change in valuation allowance 4,778 7,214 (11,531 ) Income tax (benefit) expense $ — $ — $ —
Schedule of Significant Components of Deferred Tax Assets	Significant components of our deferred tax assets are summarized as follows (in thousands): December 31, 2019 2018 Deferred tax assets: Net operating loss carryforwards $ 38,180 $ 32,997 Capitalized research and development expenses 16,900 17,279 Research credits and other state credits 12,452 11,962 Intangible assets 1,841 2,024 Reserve and accruals 2,310 2,667 Lease liability 631 — Valuation allowance (71,702 ) (66,929 ) Total deferred tax assets $ 612 $ — Deferred tax liabilities: Right of use lease assets (612 ) — Total deferred tax liabilities (612 ) — Net deferred tax assets $ — $ —
Schedule of Activity Related to Unrecognized Tax Benefits	The activity related to our unrecognized tax benefits is summarized as follows (in thousands): December 31, 2019 2018 2017 Balance as of beginning of year $ 19,643 $ 16,558 $ 13,000 Increase (decrease) related to prior year tax positions — 2 (189 ) Increase related to current year tax positions 1,659 3,083 3,747 Balance as of end of year $ 21,302 $ 19,643 $ 16,558

Quarterly Financial Data (Una_2

Quarterly Financial Data (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2019
Quarterly Financial Data [Abstract]
Summary of Quarterly Financial Data	The following financial information reflects all normal recurring adjustments, which are, in our opinion, necessary for a fair statement of the results of the interim periods. Summarized quarterly data for 2019 and 2018 are as follows (in thousands, except per share data): For the quarters ended March 31 June 30 September 30 December 31 2019: Operating expenses $ 5,877 $ 5,735 $ 5,682 $ 6,106 Net loss attributable to aTyr Pharma, Inc. (6,137 ) (5,848 ) (5,645 ) (5,973 ) Basic and diluted net loss per share $ (2.54 ) $ (1.80 ) $ (1.47 ) (1.54 ) 2018: Operating expenses $ 10,220 $ 9,960 $ 6,677 $ 5,963 Net loss attributable to aTyr Pharma, Inc. (10,667 ) (10,412 ) (7,114 ) (6,322 ) Basic and diluted net loss per share $ (5.01 ) $ (4.88 ) $ (3.33 ) (2.92 )

Organization, Business and Ba_2

Organization, Business and Basis of Presentation - Additional Information (Detail) $ in Thousands	1 Months Ended				12 Months Ended
	Feb. 29, 2020USD ($)	Jan. 31, 2020USD ($)	Jun. 30, 2019	May 31, 2018USD ($)Employee	Dec. 31, 2019USD ($)Segment	Dec. 31, 2018USD ($)
Description Of Business [Line Items]
Reverse stock split			1-for-14
Accumulated deficit					$ 322,304	$ 298,701
Cash, cash equivalents and available-for-sale investments					$ 31,100
Number of operating segment | Segment					1
ATYR1923 Manufacturer [Member] | Restructuring Plan [Member]
Description Of Business [Line Items]
Restructuring plan, percentage of reduction in total workforce				30.00%
Number of full-time employees | Employee				42
Restructuring plan, description				In May 2018, we implemented a corporate restructuring and program prioritization plan (Restructuring Plan) to streamline our operations and concentrate development efforts on the advancement of our therapeutic candidate, ATYR1923. In connection with the Restructuring Plan, we reduced our workforce by approximately 30% to 42 full-time employees. We completed the workforce reduction in June 2018.
ATYR1923 Manufacturer [Member] | Restructuring Plan [Member] | Employee Severance and Other Related Termination Benefits [Member]
Description Of Business [Line Items]
Restructuring charges				$ 900
ATYR1923 Manufacturer [Member] | Restructuring Plan [Member] | One-time Termination Benefits [Member]
Description Of Business [Line Items]
Non-cash stock-based compensation charges				$ 400
Subsequent Event [Member]
Description Of Business [Line Items]
Upfront payment received		$ 8,000
Subsequent Event [Member] | Public Offering [Member]
Description Of Business [Line Items]
Gross proceeds from underwritten follow-on public offering, including over-allotment	$ 20,700
Pangu BioPharma [Member] | Hong Kong [Member]
Description Of Business [Line Items]
Majority-owned subsidiary percentage					98.00%

Summary of Significant Accoun_4

Summary of Significant Accounting Policies - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Jan. 01, 2019
Significant Accounting Policies [Line Items]
Impairment charges on investment securities	$ 0
Aggregate value of investment securities	21,900,000	$ 26,600,000
Unrealized gain (loss) between amortized cost and fair value of investment securities	8,500	$ (10,000)
Impairment of long lived assets	0
Preferred stock redemption value	0
Operating lease, right-of-use asset	2,821,000		$ 3,500,000
Operating lease, liability	$ 2,994,000		3,500,000
ASU 2016-02 [Member]
Significant Accounting Policies [Line Items]
Operating lease, right-of-use asset			3,500,000
Operating lease, liability			$ 3,500,000
Maximum [Member]
Significant Accounting Policies [Line Items]
Maturity period of investment securities	1 year	1 year
Estimated useful life of property and equipment	7 years
Minimum [Member]
Significant Accounting Policies [Line Items]
Estimated useful life of property and equipment	3 years
Percentage of tax benefit to be realized upon settlement	50.00%

Summary of Significant Accoun_5

Summary of Significant Accounting Policies - Schedule of Potentially Dilutive Securities Not Included in Calculation of Diluted Net Loss Per Share (Detail) - shares	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not included in calculation of diluted net loss per share	966,860	1,667,923	1,629,864
Class X Preferred Stock (if-converted to common stock) [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not included in calculation of diluted net loss per share	587,445	816,851	816,851
Common Stock Warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not included in calculation of diluted net loss per share	13,904	477,639	477,639
Common Stock Options and Restricted Stock Units [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not included in calculation of diluted net loss per share	363,553	371,823	333,154
Employee Stock Purchase Plan [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Anti-dilutive securities not included in calculation of diluted net loss per share	1,958	1,610	2,220

Summary of Significant Accoun_6

Summary of Significant Accounting Policies - Summary of Net Loss Per Share (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Numerator:
Net loss attributable to aTyr Pharma, Inc.	$ (5,973)	$ (5,645)	$ (5,848)	$ (6,137)	$ (6,322)	$ (7,114)	$ (10,412)	$ (10,667)	$ (23,603)	$ (34,515)	$ (48,207)
Denominator:
Weighted average common shares outstanding									3,355,600	2,141,961	1,845,294
Weighted average common shares subject to repurchase											(261)
Weighted average common shares outstanding - basic and diluted									3,355,600	2,141,961	1,845,033
Net loss per share - basic and diluted	$ (1.54)	$ (1.47)	$ (1.80)	$ (2.54)	$ (2.92)	$ (3.33)	$ (4.88)	$ (5.01)	$ (7.03)	$ (16.11)	$ (26.13)

Fair Value Measurements - Sched

Fair Value Measurements - Schedule of Assets and Liabilities Measured at Fair Value on Recurring Basis (Detail) - Fair Value, Measurements, Recurring [Member] - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	$ 8,248	$ 16,019
Total assets measured at fair value	30,182	42,602
Available-for-sale [Member] | Short-term Investments [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	21,934	26,583
Available-for-sale [Member] | Short-term Investments [Member] | Asset-backed Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	6,304	7,773
Available-for-sale [Member] | Short-term Investments [Member] | Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	7,568	6,144
Available-for-sale [Member] | Short-term Investments [Member] | Corporate Debt Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	8,062	12,666
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Cash equivalents	8,248	16,019
Total assets measured at fair value	8,248	16,019
Significant Other Observable Inputs (Level 2) [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Total assets measured at fair value	21,934	26,583
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	21,934	26,583
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Asset-backed Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	6,304	7,773
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Commercial Paper [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	7,568	6,144
Significant Other Observable Inputs (Level 2) [Member] | Available-for-sale [Member] | Short-term Investments [Member] | Corporate Debt Securities [Member]
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]
Investments, fair value	$ 8,062	$ 12,666

Fair Value Measurements - Sch_2

Fair Value Measurements - Schedule of Available-for-sale Investments (Detail) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Schedule of Available-for-sale Securities [Line Items]
Market Value	$ 21,900	$ 26,600
Short-term Investments [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	21,924	26,593
Gross Unrealized Gains	10
Gross Unrealized Losses		(10)
Market Value	21,934	26,583
Short-term Investments [Member] | Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	7,568	6,144
Market Value	7,568	6,144
Short-term Investments [Member] | Asset-backed Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	6,299	7,777
Gross Unrealized Gains	5
Gross Unrealized Losses		(4)
Market Value	6,304	7,773
Short-term Investments [Member] | Corporate Debt Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Gross Amortized Cost	8,057	12,672
Gross Unrealized Gains	5
Gross Unrealized Losses		(6)
Market Value	$ 8,062	$ 12,666

Fair Value Measurements - Addit

Fair Value Measurements - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2019
Maximum [Member]
Schedule of Available-for-sale Securities [Line Items]
Available-for-sale investments effective maturity period	12 months

License Agreement - Additional

License Agreement - Additional Information (Detail)	1 Months Ended		12 Months Ended
	May 31, 2019USD ($)	Mar. 31, 2019USD ($)Program	Dec. 31, 2019USD ($)
Research And Development Arrangement Contract To Perform For Others [Line Items]
Revenue			$ 422,000
Collaboration Revenue [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Revenue			422,000
Research Collaboration and Option Agreement [Member] | CSL Behring [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Number of programs | Program		4
Maximum option fees receivable based on achievement of research milestones per program		$ 4,250,000
Maximum option fees receivable based on achievement of research milestones		$ 17,000,000
Proceeds from research and development funded	$ 600,000
Termination notice period		45 days
Upfront payment received	$ 600,000
Research Collaboration and Option Agreement [Member] | CSL Behring [Member] | Collaboration Revenue [Member]
Research And Development Arrangement Contract To Perform For Others [Line Items]
Revenue			$ 422,000

License Agreement - Additiona_2

License Agreement - Additional Information (Detail 1)	Dec. 31, 2019
Research Collaboration and Option Agreement [Member] | CSL Behring [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date: 2020-01-01
Research And Development Arrangement Contract To Perform For Others [Line Items]
Performance obligations period	45 days

Balance Sheet Details - Summary

Balance Sheet Details - Summary of Property and Equipment (Detail) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Property Plant And Equipment [Line Items]
Property and equipment, Gross	$ 7,484	$ 7,877
Less accumulated depreciation and amortization	(6,214)	(6,024)
Property and equipment, Net	1,270	1,853
Computer and Office Equipment [Member]
Property Plant And Equipment [Line Items]
Property and equipment, Gross	543	543
Scientific and Laboratory Equipment [Member]
Property Plant And Equipment [Line Items]
Property and equipment, Gross	5,241	5,631
Tenant Improvements [Member]
Property Plant And Equipment [Line Items]
Property and equipment, Gross	$ 1,700	$ 1,703

Balance Sheet Details - Additio

Balance Sheet Details - Additional Information (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Property Plant And Equipment [Abstract]
Depreciation expense	$ 635	$ 746	$ 713

Balance Sheet Details - Summa_2

Balance Sheet Details - Summary of Accrued Expenses (Detail) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Accrued Liabilities Current [Abstract]
Accrued salaries, wages and benefits	$ 1,275	$ 1,309
Other accrued expenses	1,101	717
Accrued expenses	$ 2,376	$ 2,026

Debt, Commitments and Conting_3

Debt, Commitments and Contingencies - Additional Information (Detail)	Nov. 01, 2018	Dec. 31, 2017USD ($)$ / sharesshares	Jun. 30, 2017USD ($)$ / sharesshares	Nov. 30, 2016USD ($)Tranche$ / sharesshares	Jun. 30, 2019	Dec. 31, 2019USD ($)	Dec. 31, 2018USD ($)	Dec. 31, 2017USD ($)$ / sharesshares	Jan. 01, 2019USD ($)
Debt Instrument [Line Items]
Loan and security agreement, payment term						Issuable in three separate tranches (the Term Loans), $10.0 million of which was funded in November 2016, $5.0 million of which was funded in June 2017 and $5.0 million of which was funded in December 2017.
Lease, practical expedients, package					true
Operating lease, right-of-use asset						$ 2,821,000			$ 3,500,000
Operating lease, liability						$ 2,994,000			$ 3,500,000
Operating lease, discount rate						9.60%
Rent expense						$ 1,000,000	$ 1,000,000	$ 900,000
Operating lease, weighted average remaining lease term						3 years 4 months 24 days
Operating lease, weighted average discount rate						9.60%
Research and development expenses						$ 14,048,000	20,385,000	30,067,000
The Scripps Research Institute [Member]
Debt Instrument [Line Items]
Termination of research funding and option agreement effective month and year	2018-11
Research Funding and Option Agreement [Member] | The Scripps Research Institute [Member]
Debt Instrument [Line Items]
Research and development expenses							$ 1,700,000	1,800,000
Silicon Valley Bank and Solar Capital, Ltd. [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement				$ 20,000,000
Number of tranches | Tranche				3
Term loan, principal outstanding before deducting debt issuance cost						7,300,000
Term loan, debt issuance costs						100,000
Accretion of final payment of debt instrument						$ 1,800,000
Warrants expiration year						7 years
Aggregate fair value of warrants using black scholes option pricing model		$ 500,000						500,000
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche One [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement				$ 10,000,000
Loan and security agreement funded date				Nov. 30, 2016
Exercise price of warrant per share | $ / shares				$ 43.93
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche One [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares				3,415
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Two [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement			$ 5,000,000
Loan and security agreement funded date			Jun. 30, 2017
Exercise price of warrant per share | $ / shares			$ 50.37
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Two [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares			1,489
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Three [Member]
Debt Instrument [Line Items]
Available credit under loan and security agreement		$ 5,000,000						$ 5,000,000
Loan and security agreement funded date		Dec. 31, 2017
Exercise price of warrant per share | $ / shares		$ 51.98						$ 51.98
Silicon Valley Bank and Solar Capital, Ltd. [Member] | Term Loans Tranche Three [Member] | Common Stock [Member]
Debt Instrument [Line Items]
Warrants to purchase number of common stock, shares | shares		1,443						1,443
Loan Amendment Agreement with SVB and Solar [Member]
Debt Instrument [Line Items]
Loan and security agreement, payment term						Under the Loan Agreement, we are obligated to make interest only payments through June 1, 2018, followed by consecutive equal monthly payments of principal and interest in arrears through the maturity date of November 18, 2020. Accordingly, we started paying the Term Loans in June 2018.
Maturity date						Nov. 18, 2020
Percentage of funded amounts for final payment				8.75%
Loan Amendment Agreement with SVB and Solar [Member] | Prime Rate [Member]
Debt Instrument [Line Items]
Interest rate spread on variable rate				4.10%
Loan Amendment Agreement with SVB and Solar [Member] | Minimum [Member]
Debt Instrument [Line Items]
Prepayment fee percentage				1.00%
Loan Amendment Agreement with SVB and Solar [Member] | Maximum [Member]
Debt Instrument [Line Items]
Prepayment fee percentage				3.00%

Debt, Commitments and Conting_4

Debt, Commitments and Contingencies - Schedule of Future Minimum Payments under Non-cancelable Operating Lease and Reconciliation to Operating Lease Liability (Detail) - USD ($) $ in Thousands	Dec. 31, 2019	Jan. 01, 2019
Leases Operating [Abstract]
2020	$ 1,002
2021	1,031
2022	1,062
2023	404
Less: Amount representing interest	(505)
Present value of lease payments	2,994	$ 3,500
Less: Current portion of operating lease liability	(755)
Long-term operating lease liability	$ 2,239

Stockholders' Equity - Addition

Stockholders' Equity - Additional Information (Detail) - USD ($)

Aug. 31, 2017

Feb. 29, 2020

Jan. 31, 2020

Apr. 30, 2019

Jan. 31, 2019

Jul. 31, 2018

Apr. 30, 2015

Dec. 31, 2019

Dec. 31, 2018

Dec. 31, 2017

Jan. 01, 2020

May 31, 2019

Mar. 31, 2019

Jan. 01, 2019

Jan. 01, 2018

Jan. 01, 2017

Jun. 30, 2016

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Preferred stock, par value

$ 0.001

$ 0.001

Number of common stock shares reserved for issuance

1,304,598

Stock options granted

76,722

Weighted average exercise price, granted

$ 7.15

Weighted average grant date fair value of options granted

$ 5.67

$ 25.76

$ 39.95

Total grant date fair value of restricted stock units vested

$ 39,000

$ 200,000

$ 100,000

Aggregate intrinsic value of stock options exercised

6,000

300,000

Aggregate intrinsic value of restricted stock units

31,000

$ 19,000

$ 100,000

Unrecognized share based compensation expense related to unvested stock options

2,400,000

Unrecognized share based compensation expense related to restricted stock units

$ 100,000

Employee Stock Option [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Unrecognized cost expected to be recognized over a weighted average period

2 years 3 months 18 days

Restricted Stock Unit [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Unrecognized cost expected to be recognized over a weighted average period

8 months 12 days

2014 Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Maximum term for stock option plan grant

10 years

Options vesting period

4 years

2015 Stock Option and Incentive Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Maximum term for stock option plan grant

10 years

Options vesting period

4 years

Options vesting period, description

For an initial grant to an employee, 25% of the options generally vest on the first anniversary of the original vesting date, with the balance vesting monthly over the remaining three years. For subsequent grants to an employee, the options generally vest monthly over a four-year term.

2015 Stock Option and Incentive Plan [Member] | One Year Anniversary [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Option vesting percentage

25.00%

2015 Employee Stock Purchase Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Number of common stock shares reserved for issuance

78,697

Class X Convertible Preferred Stock [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Preferred stock, shares issued

1,643,961

2,285,952

VGO Fund [Member] | Subsequent Event [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Convertible preferred stock, common stock issued upon conversion

179,197

408,247

VGO Fund [Member] | Class X Convertible Preferred Stock [Member] | Subsequent Event [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Converted shares of preferred stock

501,483

1,142,478

Common Stock [Member] | Chief Financial Officer [Member] | Inducement Pool Non-Qualified Option [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Options vesting period

4 years

Stock options granted

14,285

Weighted average exercise price, granted

$ 11.41

Common Stock [Member] | One Year Anniversary [Member] | Chief Financial Officer [Member] | Inducement Pool Non-Qualified Option [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Options vesting period

1 year

Option vesting percentage

25.00%

Common Stock [Member] | Monthly Basis Over Three Years [Member] | Chief Financial Officer [Member] | Inducement Pool Non-Qualified Option [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Options vesting period

3 years

Option vesting percentage

75.00%

Common Stock [Member] | Federated Kaufmann Small Cap Fund | Securities Purchase Agreement [Member] | Institutional Investor [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued during the period

660,154

Shares issued, price per share

$ 7.57

Net proceeds from issuance of common stock

$ 5,000,000

ATM Offering Program [Member] | Cowen Company, LLC (Cowen) [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Net proceeds from issuance of common stock

$ 1,400,000

ATM Offering Program [Member] | Cowen Company, LLC (Cowen) [Member] | Sale Agreement [Member] | Maximum [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Agreed upon value of sale of common stock per transaction

$ 35,000,000

ATM Offering Program [Member] | Common Stock [Member] | Cowen Company, LLC (Cowen) [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued during the period

193,670

Shares issued, price per share

$ 7.35

ATM Offering Program [Member] | H.C. Wainwright & Co., LLC [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Net proceeds from issuance of common stock

$ 3,000,000

Commission rate equal to gross proceeds

3.00%

ATM Offering Program [Member] | H.C. Wainwright & Co., LLC [Member] | Sale Agreement [Member] | Maximum [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Agreed upon value of sale of common stock per transaction

$ 10,000,000

ATM Offering Program [Member] | Common Stock [Member] | H.C. Wainwright & Co., LLC [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued during the period

611,687

Shares issued, price per share

$ 5.43

Private Placement [Member] | VGO Fund [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Convertible preferred stock, common stock issued upon conversion

229,283

Private Placement [Member] | VGO Fund [Member] | Securities Purchase Agreement [Member] | Class X Convertible Preferred Stock [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued, price per share

$ 13.25

Preferred stock, shares issued

2,285,952

Preferred stock, par value

$ 0.001

Convertible preferred stock terms of conversion

Each share of preferred stock is convertible into approximately 0.357 shares of our common stock. In January 2019, the VGO Fund converted 641,991 shares of its preferred stock into 229,283 shares of common stock.

Convertible preferred stock, common stock issued upon conversion

0.357

Converted shares of preferred stock

641,991

Private Placement [Member] | Remaining Purchasers [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Warrants to purchase number of common stock, shares

463,735

Gross proceeds from transaction

$ 45,800,000

Private Placement [Member] | Common Stock [Member] | VGO Fund [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued during the period

126,985

Shares issued, price per share

$ 37.10

Private Placement [Member] | Common Stock [Member] | Remaining Purchasers [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Shares issued during the period

292,453

Shares issued, price per share

$ 37.10

Private Placement [Member] | Common Stock [Member] | Remaining Purchasers [Member] | Maximum [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Warrants to purchase number of common stock, shares

109,743

Private Placement [Member] | Warrants [Member] | Remaining Purchasers [Member] | Securities Purchase Agreement [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Exercise price of warrant per share

$ 64.92

Warrants expiration date

Dec. 31, 2019

IPO [Member] | 2015 Stock Option and Incentive Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Effective date of plan

May 6, 2015

Number of common stock shares reserved for issuance

112,399

Stock option grants description

The number of shares reserved and available for issuance under the 2015 Plan will automatically increase each January 1, beginning on January 1, 2016 and thereafter until January 1, 2019, by the lesser of (i) 1,840,000 shares, (ii) 4% of the outstanding number of shares of our common stock on the immediately preceding December 31 or (iii) an amount determined by our board of directors.

Percentage threshold of outstanding shares as of December 31 of each year for calculation of annual increase in authorized shares under the plan

4.00%

Additional number of common stock shares reserved for issuance

71,428

87,368

85,111

67,842

IPO [Member] | 2015 Stock Option and Incentive Plan [Member] | Subsequent Event [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Number of common stock shares reserved for issuance

260,999

IPO [Member] | 2015 Employee Stock Purchase Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Effective date of plan

May 6, 2015

Number of common stock shares reserved for issuance

16,258

Percentage threshold of outstanding shares as of December 31 of each year for calculation of annual increase in authorized shares under the plan

1.00%

Additional number of common stock shares reserved for issuance

21,842

21,277

16,960

IPO [Member] | 2015 Employee Stock Purchase Plan [Member] | Subsequent Event [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Number of common stock shares reserved for issuance

78,697

IPO [Member] | Maximum [Member] | 2015 Stock Option and Incentive Plan [Member]

Share Based Compensation Arrangement By Share Based Payment Award [Line Items]

Annual increase in shares authorized under plan, shares threshold

131,428

Stockholders' Equity - Summary

Stockholders' Equity - Summary of Stock Option Activity (Detail)	12 Months Ended
	Dec. 31, 2019USD ($)$ / sharesshares
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Number of Outstanding Options, Beginning Balance | shares	356,353
Number of Outstanding Options, Granted | shares	76,722
Number of Outstanding Options, Canceled/forfeited/expired | shares	(81,997)
Number of Outstanding Options, Ending Balance | shares	351,078
Number of Outstanding Options, Vested and Expected to Vest, Ending Balance | shares	351,078
Number of Outstanding Options, Exercisable, Ending Balance | shares	218,021
Weighted Average Exercise Price, Beginning Balance | $ / shares	$ 62.61
Weighted Average Exercise Price, Granted | $ / shares	7.15
Weighted Average Exercise Price, Canceled/forfeited/expired | $ / shares	58.98
Weighted Average Exercise Price, Ending Balance | $ / shares	51.34
Weighted Average Exercise Price, Options Vested and Expected to Vest, Ending Balance | $ / shares	51.34
Weighted Average Exercise Price, Options Exercisable, Ending Balance | $ / shares	$ 67.82
Weighted Average Contractual Term, Outstanding	6 years 7 months 6 days
Weighted Average Contractual Term, Options Vested and Expected to Vest	6 years 7 months 6 days
Weighted Average Contractual Term, Options Exercisable	5 years 6 months 3 days
Aggregate Intrinsic Value, Outstanding | $	$ 910
Aggregate Intrinsic Value, Options Vested and Expected to Vest | $	910
Aggregate Intrinsic Value, Options Exercisable | $	$ 45

Stockholders' Equity - Summar_2

Stockholders' Equity - Summary of Assumptions Used to Determine Fair Value of Employee Stock Option Grants, Employee Stock Purchase Plan and Performance Options with Market Condition (Detail)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
ESPP [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	6 months	6 months	6 months
Risk-free interest rate, minimum	1.60%	1.40%	0.60%
Risk-free interest rate, maximum	2.50%	2.10%	1.00%
Expected volatility, minimum	99.70%	71.50%	74.50%
Expected volatility, maximum	141.70%	99.70%	115.20%
Expected dividend yield	0.00%	0.00%	0.00%
Employee Stock Option [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Risk-free interest rate, minimum	1.40%	2.30%	1.90%
Risk-free interest rate, maximum	2.60%	3.00%	2.10%
Expected volatility, minimum	97.20%	87.90%	99.10%
Expected volatility, maximum	105.40%	98.40%	124.40%
Expected dividend yield	0.00%	0.00%	0.00%
Employee Stock Option [Member] | Minimum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	5 years 6 months 3 days	5 years	5 years 6 months
Employee Stock Option [Member] | Maximum [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Expected term (in years)	6 years 25 days	6 years 29 days	6 years 29 days

Stockholders' Equity - Schedule

Stockholders' Equity - Schedule of Restricted Stock Unit Activity (Detail) - Restricted Stock Unit [Member]	12 Months Ended
	Dec. 31, 2019$ / sharesshares
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Number of Outstanding Restricted Stock Units, Beginning Balance | shares	15,470
Number of Outstanding Restricted Stock Units, Granted | shares	5,356
Number of Outstanding Restricted Stock Units, Released | shares	(7,487)
Number of Outstanding Restricted Stock Units, Forfeited | shares	(864)
Number of Outstanding Restricted Stock Units, Ending Balance | shares	12,475
Weighted Average Grant Date Fair Value, Beginning Balance | $ / shares	$ 11.91
Weighted Average Grant Date Fair Value, Granted | $ / shares	7.24
Weighted Average Grant Date Fair Value, Released | $ / shares	11.91
Weighted Average Grant Date Fair Value, Forfeited | $ / shares	11.90
Weighted Average Grant Date Fair Value, Ending Balance | $ / shares	$ 9.90

Stockholders' Equity - Schedu_2

Stockholders' Equity - Schedule of Allocation of Stock-Based Compensation for All Options Including Performance Options with Market Condition and Restricted Stock Units (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 1,783	$ 3,431	$ 6,784
Research and Development Expense [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	354	1,216	1,399
General and Administrative Expense [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Total stock-based compensation expense	$ 1,429	$ 2,215	$ 5,385

Stockholders' Equity - Summar_3

Stockholders' Equity - Summary of Warrants Outstanding (Detail)	12 Months Ended
	Dec. 31, 2019$ / sharesshares
Class Of Warrant Or Right [Line Items]
Number Outstanding	13,904
Warrant One [Member]
Class Of Warrant Or Right [Line Items]
Number Outstanding	144
Exercise Price Per Share | $ / shares	$ 104.65
Expiration Date	2021-03
Warrant Two [Member]
Class Of Warrant Or Right [Line Items]
Number Outstanding	1,066
Exercise Price Per Share | $ / shares	$ 281.50
Expiration Date	2023-07
Warrant Three [Member]
Class Of Warrant Or Right [Line Items]
Number Outstanding	6,830
Exercise Price Per Share | $ / shares	$ 43.93
Expiration Date	2023-11
Warrant Four [Member]
Class Of Warrant Or Right [Line Items]
Number Outstanding	2,978
Exercise Price Per Share | $ / shares	$ 50.37
Expiration Date	2024-06
Warrant Five [Member]
Class Of Warrant Or Right [Line Items]
Number Outstanding	2,886
Exercise Price Per Share | $ / shares	$ 51.98
Expiration Date	2024-12

Stockholders' Equity - Summar_4

Stockholders' Equity - Summary of Common Stock Reserved for Future Issuance (Detail)	Dec. 31, 2019shares
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	1,304,598
Class X Preferred Stock (if-Converted to Common Stock) [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	587,445
Common Stock Warrants [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	13,904
Common Stock Options and Restricted Stock Units [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	363,553
Shares Available Under the 2015 Plan [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	260,999
Shares Available Under the 2015 ESPP [Member]
Share Based Compensation Arrangement By Share Based Payment Award [Line Items]
Common stock reserved for future issuance	78,697

Income Tax - Schedule of Pretax

Income Tax - Schedule of Pretax Earnings (Loss) for Domestic and Foreign Operations (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Disclosure [Abstract]
United States	$ (23,315)	$ (34,021)	$ (47,712)
Foreign	(448)	(494)	(495)
Loss before income taxes	$ (23,763)	$ (34,515)	$ (48,207)

Income Tax - Schedule of Reconc

Income Tax - Schedule of Reconciliations of the Expected Statutory Federal Income Tax (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Expected income taxes benefit at federal statutory rate	$ (4,990)	$ (7,248)	$ (16,390)
State income taxes, net of federal benefit	(19)	(14)	(13)
Permanent items and other	750	770	1,311
Research credits	(817)	(1,222)	(2,286)
Unrecognized tax benefits	327	489	914
Foreign rate differential	20	22	87
Change in tax rate	(49)	(11)	(25)
Tax cuts and Jobs Act			27,933
Change in valuation allowance	$ 4,778	$ 7,214	$ (11,531)

Income Tax - Additional Informa

Income Tax - Additional Information (Detail) - USD ($)	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax [Line Items]
Valuation allowance	$ 71,702,000	$ 66,929,000
Period of change in ownership	3 years
Percentage of change in ownership	50.00%
Unrecognized tax benefits, income tax penalties and interest accrued	$ 0	$ 0	$ 0
Change in unrecognized tax benefits	0
Federal [Member]
Income Tax [Line Items]
NOLs carryforwards	163,700,000
NOLs carryforwards not subject to expiration	51,200,000
NOLs carryforwards subject to expiration	$ 112,500,000
NOLs carryforwards expiration year	2025
Research and development credit carryforward	$ 5,000,000
Research and development credit carryforward expiration year	2026
Federal [Member] | Orphan Drug Credits [Member]
Income Tax [Line Items]
Research and development credit carryforward	$ 12,500,000
Research and development credit carryforward expiration year	2035
State [Member]
Income Tax [Line Items]
NOLs carryforwards subject to expiration	$ 163,300,000
NOLs carryforwards expiration year	2021
Research and development credit carryforward	$ 4,100,000
Foreign [Member]
Income Tax [Line Items]
NOLs carryforwards not subject to expiration	$ 8,000,000

Income Tax - Schedule of Signif

Income Tax - Schedule of Significant Components of Deferred Tax Assets (Detail) - USD ($) $ in Thousands	Dec. 31, 2019	Dec. 31, 2018
Deferred tax assets:
Net operating loss carryforwards	$ 38,180	$ 32,997
Capitalized research and development expenses	16,900	17,279
Research credits and other state credits	12,452	11,962
Intangible assets	1,841	2,024
Reserve and accruals	2,310	2,667
Lease liability	631
Valuation allowance	(71,702)	$ (66,929)
Total deferred tax assets	612
Deferred tax liabilities:
Right of use lease assets	(612)
Total deferred tax liabilities	$ (612)

Income Tax - Schedule of Activi

Income Tax - Schedule of Activity Related to Unrecognized Tax Benefits (Detail) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Income Tax Disclosure [Abstract]
Balance as of beginning of year	$ 19,643	$ 16,558	$ 13,000
Increase (decrease) related to prior year tax positions		2	(189)
Increase related to current year tax positions	1,659	3,083	3,747
Balance as of end of year	$ 21,302	$ 19,643	$ 16,558

Employee Benefits - Additional

Employee Benefits - Additional Information (Detail) - 401 (k) Plan [Member] - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Defined Contribution Plan Disclosure [Line Items]
Policy approved month and year	2015-04
Date of Policy beginning	Jun. 1, 2015
Percentage of match employee contribution	50.00%
Percentage of participants's annual salary	6.00%
Discretionary contribution	$ 0.2	$ 0.2	$ 0.2

Quarterly Financial Data (Una_3

Quarterly Financial Data (Unaudited) - Schedule of Quarterly Data for Interim Periods (Detail) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2019	Sep. 30, 2019	Jun. 30, 2019	Mar. 31, 2019	Dec. 31, 2018	Sep. 30, 2018	Jun. 30, 2018	Mar. 31, 2018	Dec. 31, 2019	Dec. 31, 2018	Dec. 31, 2017
Quarterly Financial Information Disclosure [Abstract]
Operating expenses	$ 6,106	$ 5,682	$ 5,735	$ 5,877	$ 5,963	$ 6,677	$ 9,960	$ 10,220	$ 23,400	$ 32,820	$ 47,145
Net loss attributable to aTyr Pharma, Inc.	$ (5,973)	$ (5,645)	$ (5,848)	$ (6,137)	$ (6,322)	$ (7,114)	$ (10,412)	$ (10,667)	$ (23,603)	$ (34,515)	$ (48,207)
Basic and diluted net loss per share	$ (1.54)	$ (1.47)	$ (1.80)	$ (2.54)	$ (2.92)	$ (3.33)	$ (4.88)	$ (5.01)	$ (7.03)	$ (16.11)	$ (26.13)

Subsequent Events - Additional

Subsequent Events - Additional Information (Detail) - Subsequent Event [Member] - USD ($)	Mar. 26, 2020	Feb. 29, 2020	Jan. 31, 2020	Mar. 10, 2020
Subsequent Event [Line Items]
Upfront payment received			$ 8,000,000
Pangu BioPharma [Member]
Subsequent Event [Line Items]
Grant awarded	$ 750,000
Term of project	2 years
Percentage of estimated project cost funded by grantor	50.00%
Percentage of estimated project cost funded by the company	50.00%
Public Offering [Member]
Subsequent Event [Line Items]
Gross proceeds from underwritten follow-on public offering, including over-allotment		$ 20,700,000
Public Offering [Member] | Common Stock [Member]
Subsequent Event [Line Items]
Number of shares issued and sold		4,235,294
Shares issued price per share		$ 4.25
Issuance of additional share of common stock				635,294
VGO Fund [Member]
Subsequent Event [Line Items]
Convertible preferred stock, common stock issued upon conversion		179,197	408,247
Percent ownership		6.70%
VGO Fund [Member] | Class X Convertible Preferred Stock [Member]
Subsequent Event [Line Items]
Converted shares of preferred stock		501,483	1,142,478
Development Regulatory And Sales Milestones [Member]
Subsequent Event [Line Items]
Maximum additional receivable based on achievement of research milestones			$ 167,000,000