As filed with the Securities and Exchange Commission on August 18, 2017March 17, 2023

Registration No. 333-            

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM S-3

REGISTRATION STATEMENT

UNDER

THE SECURITIES ACT OF 1933

Invitae Corporation

(Exact nameName of registrantRegistrant as specifiedSpecified in its charter)Its Charter)

1400 16th Street

San Francisco, CA 94103

(415) 374-7782

(Address, including zip code, and telephone number, including area code, of registrant’s principal executive offices)

Sean E. George, Ph.D.Kenneth D. Knight

President and Chief Executive Officer

INVITAE CORPORATIONInvitae Corporation

1400 16th Street

San Francisco, CA 94103

(415) 374-7782

(Name, address, including zip code, and telephone number, including area code, of agent for service)

Copies to:

Approximate date of commencement of proposed sale to the publicpublic:: From time to time after this registration statement becomes effective, as determined by market conditions and other factors.

If the only securities being registered on this form are being offered pursuant to dividend or interest reinvestment plans, please check the following box.  ☐

If any of the securities being registered on this form are to be offered on a delayed or continuous basis pursuant to Rule 415 under the Securities Act of 1933, other than securities offered only in connection with dividend or interest reinvestment plans, check the following box.  ☒☑

If this form is filed to register additional securities for an offering pursuant to Rule 462(b) under the Securities Act, please check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.  ☐

If this form is a post-effective amendment filed pursuant to Rule 462(c) under the Securities Act, check the following box and list the Securities Act registration statement number of the earlier effective registration statement for the same offering.  ☐

If this form is a registration statement pursuant to General Instruction I.D. or a post-effective amendment thereto that shall become effective upon filing with the Commission pursuant to Rule 462(e) under the Securities Act, check the following box.  ☐

If this form is a post-effective amendment to a registration statement filed pursuant to General Instruction I.D. filed to register additional securities or additional classes of securities pursuant to Rule 413(b) under the Securities Act, check the following box.  ☐

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer, or a smaller reporting company, or an emerging growth company. See the definitions of “large accelerated filer,” “accelerated filer” andfiler,” “smaller reporting company” and “emerging growth company” in Rule 12b-2 of the Exchange Act. (Check one):

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 7(a)(2)(B) of the Securities Act.  ☒☐

CALCULATION OF REGISTRATION FEE

The Registrantregistrant hereby amends this registration statement on such date or dates as may be necessary to delay its effective date until the Registrantregistrant shall file a further amendment which specifically states that this registration statement shall thereafter become effective in accordance with Section 8(a) of the Securities Act of 1933 or until the registration statement shall become effective on such date as the Commission, acting pursuant to said Section 8(a), may determine.

The information in this preliminary prospectus is not complete and may be changed. WeThese securities may not sell these securitiesbe sold until the registration statement filed with the Securities and Exchange Commission is effective. This preliminary prospectus is not an offer to sell these securities and is not solicitingnor does it seek an offer to buy these securities in any statejurisdiction where the offer or sale is not permitted.

Subject Toto Completion, Dated August 18, 2017dated March 17, 2023.

PROSPECTUS

5,188,235111,627,888 Shares

Invitae Corporation

Common Stock

TheThis prospectus relates to the resale from time to time by the selling stockholdersstockholder identified in this prospectus may sellof up to an aggregate of 5,188,235111,627,888 shares of our common stock.stock, $0.0001 par value per share, issuable upon conversion of our 4.5% Series B Convertible Senior Secured Notes due 2028 issued by us to the selling stockholder, or the Series B Notes, or issuable upon exercise of warrants to purchase our common stock, or the Warrants, issuable in connection with certain prepayments of the Series B Notes or our 4.5% Series A Convertible Senior Secured Notes due 2028 issued by us to the selling stockholder, or the Series A Notes, and together with the Series B Notes, the Notes, in each case pursuant to the Indenture in respect of the Notes, or the Indenture, with U.S. Bank Trust Company, National Association, as trustee and collateral agent, or the Trustee. When we refer to the selling stockholder in this prospectus, we are referring to the entities named in this prospectus as the selling stockholder and, as applicable, its permitted transferees, pledgees, assignees, distributees, donees or successors or others who later hold any of the selling stockholder’s interests. The Notes were acquired from us in a private placement that closed on March 7, 2023, and are more fully described in the section entitled “Prospectus Summary—The Transaction.” We will not receive any of the proceeds from any sale by the saleselling stockholder of the shares of our common stock offered by this prospectus and any prospectus supplement, but in some cases we have agreed to pay certain registration expenses. We will receive the selling stockholders.proceeds from any exercise of the Warrants on a cash basis.

Our registration of the shares of our common stock covered by this prospectus does not mean that the selling stockholdersstockholder will offer or sell any of the shares of our common stock. The selling stockholdersstockholder identified in this prospectus may sell the shares of our common stock covered by this prospectus in a number of different ways and at varying prices. For additionalWe provide more information on the possible methods of sale that may be used byabout how the selling stockholders, you should refer tostockholder may sell the information undersecurities in the headingsection entitled “Plan of Distribution” on page 6 of this prospectus.Distribution.”

Our common stock is listed on The New York Stock Exchange under the symbol “NVTA.” On August 18, 2017,March 16, 2023, the last reported sale price of our common stock on The New York Stock Exchange was $9.60$1.39 per share.

Investing in our securitiescommon stock involves risks. See the section entitled “Risk Factors” included oron page 3 of this prospectus and “Item 1A—Risk Factors” in our most recent Annual Report on Form 10-K that is incorporated by reference into this prospectus and in the other documents we incorporate by reference into this prospectus before making an investment decision.

Neither the Securities and Exchange Commission nor any state securities commission has approved or disapproved of these securities or passed upon the adequacy or accuracy of this prospectus. Any representation to the contrary is a criminal offense.

The date of this prospectus is , 2017March 17, 2023.

TABLE OF CONTENTS

We have notNeither we, the selling stockholder nor any underwriter, if any, has authorized anyone to provide any information other than that contained or incorporated by reference ininto this prospectus, any applicable prospectus supplement or any free writing prospectus prepared by or on behalf of us or to which we have referred you. We take noyou, and you should not rely on any other information. Neither we, the selling stockholder nor any underwriter, if any, takes any responsibility for, and none of the foregoing can provide noany assurance as to the reliability of, any other information that others may give you. We are not making an offer to sell these securities in any jurisdiction where the offer or sale is not permitted. You should assume that the information in this prospectus and any prospectus supplement, or incorporated by reference herein or therein, is accurate only as of the dates of those documents. Our business, financial condition, results of operations and prospects may have changed since those dates.

ABOUT THIS PROSPECTUS

Unless the context otherwise requires, references inYou should read this prospectus and any prospectus supplement for a specific offering of securities, together with additional information described in the section entitled “Where You Can Find More Information” below, before making an investment decision. If there is any inconsistency between this prospectus and the information contained in a prospectus supplement or any free writing prospectus prepared by or on behalf of us to “Invitae,” “we,” “us” and “our” refer to Invitae Corporation and its subsidiaries.which we have referred you, you should rely on the information in the prospectus supplement or such free writing prospectus.

When we refer toInformation about the selling stockholdersstockholder may change over time. Any changed information given to us by the selling stockholder will be set forth in thisa prospectus wesupplement if and when necessary. Further, in some cases, the selling stockholder will also be required to provide a prospectus supplement containing specific information about the terms on which they are referring to the stockholders identified in the table under the heading “Selling Stockholders” herein as well as any donees, pledgees, transferees or other successors-in-interest that receivedoffering and selling shares of our common stock afterstock. If a prospectus supplement is provided and the datedescription of the offering in the prospectus supplement varies from the information in this prospectus, fromyou should rely on the selling stockholders pursuant to a gift, a pledge, a partnership distribution or other transfer (other than a public sale).information in the prospectus supplement.

Invitae and the Invitae logo are our trademarks. This prospectus and the documents incorporated by reference into this prospectus may also contain trademarks and trade names that are the property of their respective owners. We do not intend our use or display of other companies’ trade names, trademarks or service marks

Unless the context otherwise requires, references in this prospectus to imply relationships with, or endorsements or sponsorship of us by, these other companies.“Invitae,” “we,” “us” and “our” refer to Invitae Corporation and its subsidiaries.

RISK FACTORS

Investing in our common stock involves a high degree of risk. You should carefully consider the risk factors described below, as well as the risk factors discussed under the caption “Risk Factors” in our most recent Annual Report on Form 10-K, Quarterly Reports on Form 10-Q or Current Reports on Form 8-K, as well as any prospectus supplement to this prospectus, and the other information contained in or incorporated by reference into this prospectus and any prospectus supplement to this prospectus before deciding to invest in our common stock. The risks and uncertainties described below are not the only ones we face. Additional risks and uncertainties not presently known to us or that we currently deem immaterial may also impair our business operations. If any of these risks actually occur, our business, financial condition and results of operations could be materially and adversely affected.

Our stock price is volatile, and you may not be able to sell shares of our common stock at or above the price you paid.

The trading price of our common stock is volatile and could be subject to wide fluctuations in response to various factors, some of which are beyond our control. These factors include:

In addition, the stock market in general, and the market for stock of life sciences companies in particular, has experienced extreme price and volume fluctuations that have often been unrelated or disproportionate to the operating performance of those companies. Broad market and industry factors may seriously affect the market price of our common stock, regardless of our actual operating performance. Moreover, in the past, following periods of volatility in the overall market and the market price of a particular company’s securities, securities class action litigation has often been instituted against these companies. This litigation, if instituted against us, could result in substantial costs and a diversion of our management’s attention and resources.

If securities or industry analysts issue an adverse opinion regarding our stock or do not publish research or reports about our company, our stock price and trading volume could decline.

The trading market for our common stock will depend in part on the research and reports that equity research analysts publish about us and our business. We do not control these analysts or the content and opinions included in their reports. Securities analysts may elect not to provide research coverage of our company and such lack of research coverage may adversely affect the market price of our common stock. The price of our common stock could also decline if one or more equity research analysts downgrade our common stock, change their price targets, issue other unfavorable commentary or cease publishing reports about us or our business. If one or more equity research analysts cease coverage of our company, we could lose visibility in the market, which in turn could cause our stock price to decline.

Sales of a substantial number of shares of our common stock in the public market could cause our stock price to fall.

Sales of a substantial number of shares of our common stock in the public market or the perception that these sales might occur could depress the market price of our common stock and could impair our ability to raise capital through the sale of additional equity securities. We are unable to predict the effect that sales may have on the prevailing market price of our common stock. In addition, the sale of substantial amounts of our common stock could adversely impact its price. As of December 31, 2022, we had outstanding 245,562,121 shares of our common stock, options to purchase 2,382,822 shares of our common stock (of which 1,383,848 were exercisable as of that date) and restricted stock units, or RSUs, representing 11,895,412 shares of our common stock (which includes an estimated number of RSUs, subject to certain employees’ continued service with us, or time-based RSUs, and RSUs that are performance based RSUs granted in connection with an acquisition). The foregoing does not include 8,791,334 shares of our common stock that may be issuable in connection with indemnification hold-backs and contingent consideration related to our acquisitions, shares that may be issuable in the future in connection with approximately $44 million aggregate principal amount of our convertible senior notes due 2024 and $1,150 million aggregate principal amount of our convertible senior notes due 2028, 14,219,859 shares that we issued in connection with the closing of the transactions contemplated by the Exchange Agreement and the Other Exchange Agreements, shares that may be issuable in the future in connection with the Notes and the Other Holder Notes, including the 111,627,888 shares that we are registering for resale by this prospectus, or shares issuable pursuant to our Sales Agreement with Cowen and Company, LLC, dated as of May 4, 2021. In addition, as of December 31, 2022, 5,499,674 and 2,149,066 shares of common stock are available for future issuance under our 2015 Stock Incentive Plan and Employee Stock Purchase Plan, respectively, and as of January 1, 2023, 9,822,484 and 2,455,621 additional shares of common stock became available for future issuance under our 2015 Stock Incentive Plan and our Employee Stock Purchase Plan, respectively. The sale or the availability for sale of a large number of shares of our common stock in the public market could cause the price of our common stock to decline.

We have never paid dividends on our capital stock, and we do not anticipate paying dividends in the foreseeable future.

We have never paid dividends on any of our capital stock and currently intend to retain any future earnings to fund the growth of our business. In addition, the terms of our credit agreement restrict our ability to pay dividends. Any determination to pay dividends in the future will be at the discretion of our board of directors and will depend on our financial condition, operating results, capital requirements, general business conditions and other factors that our board of directors may deem relevant. As a result, capital appreciation, if any, of our common stock will be the sole source of gain for the foreseeable future.

Anti-takeover provisions in our charter documents and under Delaware law could discourage, delay or prevent a change in control and may affect the trading price of our common stock.

Provisions in our restated certificate of incorporation and our amended and restated bylaws may have the effect of delaying or preventing a change of control or changes in our management. Our restated certificate of incorporation and amended and restated bylaws include provisions that:

In addition, we are subject to the provisions of Section 203 of the Delaware General Corporation Law regulating corporate takeovers. Section 203 generally prohibits us from engaging in a business combination with an interested stockholder subject to certain exceptions.

Our certificate of incorporation designates the Court of Chancery of the State of Delaware as the sole and exclusive forum for certain types of actions and proceedings that may be initiated by our stockholders, which could limit our stockholders’ ability to obtain a favorable judicial forum for disputes with us or our directors, officers or other employees.

Our certificate of incorporation provides that, unless we consent in writing to the selection of an alternative forum, the Court of Chancery of the State of Delaware shall be the sole and exclusive forum for:

Section 27 of the Securities Exchange Act of 1934, or the Exchange Act, creates exclusive federal jurisdiction over all suits brought to enforce any duty or liability created by the Exchange Act or the rules and regulations thereunder. As a result, the exclusive forum provision in our certificate of incorporation will not apply to suits brought to enforce any duty or liability created by the Exchange Act or any other claim for which the federal courts have exclusive jurisdiction. Section 22 of the Securities Act creates concurrent jurisdiction for federal and state courts over all suits brought to enforce any duty or liability created by the Securities Act or the rules and regulations thereunder. As a result, the exclusive forum provision in our certificate of incorporation will

not apply to suits brought to enforce any duty or liability created by the Securities Act or any other claim for which the federal and state courts have concurrent jurisdiction.

Any person or entity purchasing or otherwise acquiring any interest in shares of our capital stock shall be deemed to have notice of and consented to the provisions of our certificate of incorporation described above. This choice of forum provision may limit a stockholder’s ability to bring a claim in a judicial forum that it finds favorable for disputes with us or our directors, officers or other employees, which may discourage such lawsuits against us and our directors, officers and other employees. Alternatively, if a court were to find these provisions of our certificate of incorporation inapplicable to, or unenforceable in respect of, one or more of the specified types of actions or proceedings, we may incur additional costs associated with resolving such matters in other jurisdictions, which could adversely affect our business, financial condition or results of operations.

FORWARD-LOOKING STATEMENTS

When used in thisThis prospectus and the wordsdocuments we have filed with the Securities and Exchange Commission, or the SEC, that are incorporated herein by reference contain “forward-looking statements” within the meaning of Section 27A of the Securities Act and Section 21E of the Exchange Act that involve risks and uncertainties. These statements relate to future periods, future events or our future operating or financial plan or performance. These statements can often be identified by the use of forward-looking terminology such as “expects,” “believes,” “intends,” “anticipates,” “estimates,” “plans,” “may,” “could,or “will,” “intends,”or the negative of these terms, and other similar expressionsexpressions. These forward-looking statements reflect our current views with respect to future events, are intended to identify forward-looking statements. These statementsbased on assumptions and are subject to knownrisks and unknownuncertainties. These risks and uncertainties that could cause actual results to differ materially from those projectedprojected. We discuss many of these risks and uncertainties in greater detail in the section entitled “Risk Factors” and in the documents that are incorporated by reference into this prospectus, which address additional factors that could cause results or otherwise implied byevents to differ from those set forth in the forward-looking statements. These forward-looking statements speak only as of the date of this prospectus. Given these risks and uncertainties, you should not place undue reliance on these forward-looking statements. We will discuss many of these risks and uncertainties in greater detail in any prospectus supplement under the heading “Risk Factors.” Additional cautionary statements or discussions of risks and uncertainties that could affect our results or the achievement of the expectations described in forward-looking statements may also be contained in the documentsExcept as required by federal securities laws, we incorporate by reference into this prospectus.

These forward-looking statements speak only as of the date of this prospectus. We expressly disclaim anyundertake no obligation or undertaking to release publicly any updates or revisions toupdate any forward-looking statements contained herein to reflectfor any changereason, even if new information becomes available or other events occur in our expectations with regard thereto or any change in events, conditions or circumstances on which any such statement is based. You should, however, review additional disclosures we make in our Annual Report on Form 10-K, Quarterly Reports on Form 10-Q, and Current Reports on Form 8-K filed with the Securities and Exchange Commission, or SEC.future.

USE OF PROCEEDS

All of the shares of common stock being offered hereby are being sold by the selling stockholder identified in this prospectus. We will not receive any proceeds from the sale of common stock by the selling stockholders. Allstockholder. We will receive the proceeds from any exercise of the Warrants on a cash basis. We intend to use the proceeds from the saleexercise of the shares will beWarrants on a cash basis, if any, for the accounts of the selling stockholders. See “Selling Stockholders”general corporate and “Plan of Distribution.”working capital purposes.

SELLING STOCKHOLDERSSTOCKHOLDER

On August 3, 2017, we sold to theThe selling stockholders 5,188,235 shares of our common stock in a private placement, pursuant to a securities purchase agreement with the selling stockholders. The registration statement to which this prospectus relates is being filed pursuant to a registration rights agreement we entered into with the selling stockholders to register the shares of our common stock soldstockholder listed in the private placement.

The following table sets forth, to our knowledge, certain information as of August 10, 2017 regarding the beneficial ownership of our common stock by the selling stockholders and the shares being offered by the selling stockholders. Beneficial ownership has been determined in accordance with the rules of the SEC. Information with respect to beneficial ownership is based upon information obtained from the selling stockholders. Information with respect to shares owned beneficially after the offering assumes the sale of all of the shares offered and no other purchases or sales of our common stock. The selling stockholdersbelow may offer and sell some, all or none of their shares.

and (vi) 26,500 shares held by Redmile Special Opportunities Fund, Ltd. Also includes an aggregate of 812,240 shares beneficially owned prior to offering consisting of (a) 465,535 shares held by Redmile Private Investments I, L.P. and (b) 346,705 shares held by Redmile Private Investments I Affiliates, L.P., which shares are not being offered hereby. Redmile Group, LLC is the investment manager of each of the private investment vehicles and separately managed accounts listed in this footnote (2) and, in such capacity, exercises sole voting and investment power over all of the shares held by such vehicles and accounts and may be deemed to be the beneficial owner of these shares. Jeremy Green serves as the managing member of Redmile Group, LLC and also may be deemed to be the beneficial owner of these shares. Redmile Group, LLC and Mr. Green each disclaims beneficial ownership of these shares, except to the extent of its or his pecuniary interest in such shares, if any.

(3)	Perceptive Advisors, LLC is the investment advisor of Perceptive Life Sciences Master Fund Ltd. Joseph E. Edelman, as the General Partner of Perceptive Advisors, LLC, has voting and investment power over all of the shares held by Perceptive Life Sciences Master Fund Ltd.

(4)

Deerfield Mgmt, L.P. is the general partner of each of Deerfield Partners, L.P. and Deerfield International Master Fund, L.P. Deerfield Management Company, L.P. is the investment manager of each of Deerfield Partners, L.P. and Deerfield International Master Fund, L.P. Mr. James E. Flynn is the sole member of the general partner of each of Deerfield Mgmt, L.P. and Deerfield Management Company, L.P. Each of Deerfield Mgmt, L.P., Deerfield Management Company, L.P. and Mr. James E. Flynn may be deemed to beneficially own all of the shares held by Deerfield Partners, L.P. and Deerfield International Master Fund, L.P.

(5)

Consists of (i) 355,500 shares held by Acuta Capital Fund, LP and (ii) 94,500 shares held by Acuta Opportunity Fund, LP. Richard Lin is the Managing Member of Acuta Capital Partners, LLC, the general partner of Acuta Capital Fund, LP and Acuta Opportunity Fund, LP, and has voting and investment power over all of the shares held by Acuta Capital Fund, LP and Acuta Opportunity Fund, LP. Mr. Lin disclaims beneficial ownership over all of the shares held by Acuta Capital Fund, LP and Acuta Opportunity Fund, LP, except to the extent of his pecuniary interest in such shares.

(6)

OrbiMed Capital GP V LLC (“GP V”) is the general partner of OrbiMed Private Investments V, LP (“OPI V”). OrbiMed Advisors LLC (“OrbiMed”) is the managing member of GP V. Samuel D. Isaly is the managing member of and owner of a controlling interest in OrbiMed. By virtue of such relationships, GP V, OrbiMed and Mr. Isaly may be deemed to have voting and investment power over all of the shares held by OPI V. Each of GP V, OrbiMed and Mr. Isaly disclaims beneficial ownership of the shares held by OPI V, except to the extent of its or his pecuniary interest in such shares, if any.

(7)

Broadfin Capital, LLC serves as investment adviser to Broadfin Healthcare Master Fund, Ltd. with the power to direct investments and/or sole power to vote the shares owned by Broadfin Healthcare Master Fund, Ltd. Kevin Kotler is the Managing Member of Broadfin Capital, LLC. Mr. Kotler has voting and investment power over all of the shares held by Broadfin Healthcare Master Fund, Ltd. Mr. Kotler disclaims beneficial ownership of all shares beneficially owned, except to the extent of his pecuniary interests in such shares.

(8)

Stonepine Capital Management, LLC is the general partner of Stonepine Capital, L.P. Jon M. Plexico and Timothy P. Lynch, the managing members of Stonepine Capital Management, LLC, have voting and investment power over all of the shares held by Stonepine Capital, L.P. and disclaim beneficial ownership of such shares, except to the extent of their pecuniary interest in such shares.

(9)	Prelude Capital Partners, LLC is the general partner of Prelude Opportunity Fund, LP. Cisco J. del Valle and Gavin Saitowitz, as managing members of Prelude Capital Partners, LLC, have voting and investment power over all of the shares held by Prelude Opportunity Fund, LP.

(10)

Includes (i) 100,573 shares held by Asymmetry Global Healthcare Fund, L.P. and (ii) 7,789 shares held by Asymmetry Global Healthcare (Master) Fund, LP. Also includes an aggregate of 35,977 shares beneficially owned prior to the offering consisting of (a) 33,395 shares held by Asymmetry Global Healthcare Fund, L.P. and (b) 2,582 shares held by Asymmetry Global Healthcare (Master) Fund, LP, which shares are not being offered hereby. Scott Kay and Chris Zellner have voting and investment power over all of the shares held by Asymmetry Global Healthcare Fund, L.P. and Asymmetry Global Healthcare (Master) Fund, LP.

(11)

Rock Springs General Partner LLC is the general partner of Rock Springs Capital Master Fund LP and Kris Jenner, Mark Bussard and Graham McPhail are the managing members of Rock Springs General Partner LLC. Rock Springs General Partner LLC and Messrs. Jenner, Bussard and McPhail, as managing members of Rock Springs General Partner LLC, may be deemed to have shared voting and dispositive power over the shares owned by Rock Springs Capital Master Fund LP.

(12)	Monashee Investment Management LLC, as the general partner of Monashee Capital Master Fund LP, has voting and investment power over all of the shares held by Monashee Capital Master Fund LP.

(13)	Victory Capital Management Inc. serves as investment adviser to the Victory RS Science Technology Fund with voting and investment power over the shares held by Victory RS Science Technology Fund.

PLAN OF DISTRIBUTION

We are registering the shares of common stock issued to the selling stockholders to permit the resale of these shares of common stock by the holders of the shares of common stock from time to time after the date of this prospectus. We will not receive any of the proceeds from the sale by the selling stockholders of the shares of common stock. We will bear all feesoffer and expenses incident to our obligation to register the shares of common stock. There can be no assurance that any selling stockholder will sell any or all of the shares of common stock registeredset forth below pursuant to this prospectus. When we refer to the selling stockholder in this prospectus, we refer to the person listed in the table below, and the pledgees, donees, transferees, assignees, successors and other permitted transferees that hold any of the selling stockholder’s interest in the shares of common stock after the date of this prospectus.

The following table sets forth certain information provided by or on behalf of the selling stockholder concerning shares of our common stock that may be offered from time to time by the selling stockholder pursuant to this prospectus. The selling stockholder identified below may have sold, transferred or otherwise disposed of all or a portion of its securities after the date on which it provided us with information regarding their securities. Any changed or new information given to us by the selling stockholder, including regarding the identity of, and the securities held by, the selling stockholder, will be set forth in a prospectus supplement or amendments to the registration statement of which this prospectus formsis a part.part, if and when necessary. The selling stockholder may sell all, some or none of such securities in this offering. See “Plan of Distribution.”

We have determined beneficial ownership in accordance with the rules of the SEC. To our knowledge, the selling stockholder has not held any position or office or had any other material relationship with us or our affiliates during the three years prior to the date of issuance and sale of the Notes.

PLAN OF DISTRIBUTION

We are registering 111,627,888 shares of common stock issuable upon conversion of the Series B Notes or exercise of the Warrants. The selling stockholder will be required to pay all underwriters’ or agents’ commissions and discounts, brokerage fees, underwriter marketing costs associated with the sale of shares of our common stock pursuant to this prospectus. We have agreed to reimburse the selling stockholder for up to $25,000 per registration pursuant to the Registration Rights Agreement in respect of the shares of common stock issuable upon conversion of the Series B Notes or exercise of the Warrants. We will also bear all other costs, fees and expenses incurred in effecting the registration of the shares of common stock covered by this prospectus, including, without limitation, all registration and filing fees, printing and delivery fees, New York Stock Exchange listing fees and fees and expenses of our counsel and our accountants.

The shares of common stock beneficially owned by the selling stockholders, which as used hereinstockholder covered by this prospectus may be offered and sold from time to time by the selling stockholder. The term “selling stockholder” includes donees, pledgees, transferees or other successors-in-interestsuccessors in interest selling shares of common stocksecurities received after the date of this prospectus from a selling stockholder as a gift, pledge, partnership distribution or other transfer, any of whom may from time to time, sell any or all of their shares of common stock on any stock exchange, market or trading facility on which the shares are traded or in private transactions directly or through one or more underwriters, broker dealers or agents. If the shares of common stock are sold through underwritersfrom time to time under the prospectus or broker-dealers,an amendment to the registration statement or supplement to the prospectus under Rule 424(b)(3) or other applicable provision of the Securities Act amending the list of selling stockholdersstockholder to include the pledgee, transferee or other successors in interest as selling stockholder under the prospectus, as appropriate. The selling stockholder will be responsible for underwriting discounts or commissions or agent’s commissions. Dispositionsact independently of us in making decisions with respect to the timing, manner and size of each sale. Such sales may be made on one or more exchanges or in the over-the-counter market or otherwise, at fixed prices atand under terms then prevailing market prices at the time of sale,or at prices related to the prevailingthen-current market price at varying prices determined at the time of sale, or atin negotiated prices. These sales may be effected in transactions which may involve crosses or block transactions.

The selling stockholdersstockholder may use anysell its shares of Common Stock by one or more of, or a combination of, the following methods when disposing of shares or interests therein:methods:

In addition, any shares that qualify for sale pursuant to Rule 144 or another exemption from registration under the Securities Act. may be sold under Rule 144 or such other exemption rather than pursuant to this prospectus. A selling stockholder that is an entity may elect to make an in-kind distribution of common stock to its members, partners, stockholders or other equityholders pursuant to the registration statement of which this prospectus isforms a part is declared effective by delivering a prospectus. To the SEC;

their affiliates. In addition, we will make copies of this prospectus (as it may be supplemented or amended from time to time) available to the selling stockholdersstockholder for the purpose of satisfying the prospectus delivery requirements of the Securities Act.Act, if applicable. The selling stockholdersstockholder may indemnify any broker-dealer that participates in

transactions involving the sale of the sharessecurities against certain liabilities, including liabilities arising under the Securities Act.

Broker dealers engaged byAt the selling stockholders may arrange for other broker dealers to participate in sales. Iftime a particular offer of securities is made, if required, a prospectus supplement will be distributed that will set forth the selling stockholders effect such transactions by selling sharesnumber of common stock to or through underwriters, broker dealers or agents, such underwriters, broker-dealers or agents may receive commissions insecurities being offered and the form of discounts, concessions or commissions from the selling stockholders or commissions from purchasersterms of the sharesoffering, including the name of common stock for whom they may act asany underwriter, dealer or agent, the purchase price paid by any underwriter, any discount, commission and other item constituting compensation, any discount, commission or concession allowed or reallowed or paid to whom they may sell as principal. Such commissions will be in amountsany dealer, and the proposed selling price to be negotiated, but, except as set forth in a supplement to this prospectus, in the case of an agency transaction will not be in excess of a customary brokerage commission in compliance with FINRA Rule 2440; and inpublic.

Under the case of a principal transaction a markup or markdown in compliance with FINRA IM-2440.

WeRegistration Rights Agreement, we have agreed to indemnify the selling stockholdersstockholder as a party thereto against certain liabilities that they may incur in connection with the sale of the securities registered hereunder, including liabilities under the Securities Act, and state securities laws, relating to contribute to payments that the registration of the shares offered by this prospectus.selling stockholder may be required to make with respect thereto.

We have agreed withto maintain the selling stockholders to keep theeffectiveness of this registration statement of which this prospectus constitutes a part effective until the earlier of (1)all such time as all of the shares covered by this prospectus held by non-affiliatessecurities have been sold pursuant to and in accordance with suchunder this registration statement or (2) the date on which all of the shares may be sold by non-affiliates without restriction pursuant to Rule 144 ofunder the Securities Act.

To the extent permitted by applicable law, the plan of distribution set forth above may be modified in a prospectus supplement or otherwise.

LEGAL MATTERS

The validity of the shares of common stock offered by this prospectus will be passed upon for us by Pillsbury Winthrop Shaw Pittman LLP.LLP, Palo Alto, California.

EXPERTS

Ernst & Young LLP, independent registered public accounting firm, has audited our consolidated financial statements included in our Annual Report on Form 10-K as amended, for the year ended December 31, 2016,2022, and the effectiveness of our internal control over financial reporting as of December 31, 2022, as set forth in their report,reports, which isare incorporated by reference in this prospectus and elsewhere in thisthe registration statement. Our consolidated financial statements are incorporated by reference in reliance on Ernst & Young LLP’s report,reports, given on their authority as experts in accounting and auditing.

WHERE YOU CAN FIND MORE INFORMATION

We have filed a registration statement on Form S-3 with the SEC under the Securities Act. This prospectus is part of the registration statement but the registration statement includes and incorporates by reference additional information and exhibits. We file annual, quarterly and current reports, proxy statements and other information with the SEC. You may read and copy the registration statement and any other document we file with the SEC at the public reference room maintained by the SEC at 100 F Street, N.E., Washington, D.C. 20549. You may obtain information on the operation of the public reference room by calling the SEC at 1-800-SEC-0330. The SEC also maintains a website that contains reports, proxy and information statements and other information regarding companies, such as ours, that file documents electronically with the SEC. The address of that website is http://www.sec.gov. The information on the SEC’s website is not part of this prospectus, and any references to this website or any other website are inactive textual references only.

The SEC permits us to “incorporate by reference” the information contained in documents we file with the SEC, which means that we can disclose important information to you by referring you to those documents rather than by including them in this prospectus. Information that is incorporated by reference is considered to be part of this prospectus and you should read it with the same care that you read this prospectus. Later information that we file with the SEC will automatically update and supersede the information that is either contained, or incorporated by reference, in this prospectus, and will be considered to be a part of this prospectus from the date those documents are filed. We have filed with the SEC, and incorporate by reference in this prospectus:

We also incorporate by reference all additional documents that we file with the SEC under the terms of Section 13(a), 13(c), 14 or 15(d) of the Exchange Act that are made after the initial filing date of the registration statement of which this prospectus is a part, and the effectiveness of the registration statement, as well as between the date of this prospectus and the termination of any offering of securitiescommon stock offered by this prospectus. We are not, however, incorporating, in each case, any documents or information that we are deemed to furnish and not file in accordance with SEC rules.

You may request a copy of any or all of the documents incorporated by reference but not delivered with this prospectus, at no cost, by writing or telephoning us at the following address and number: Investor Relations, Invitae Corporation, 1400 16th Street, San Francisco, California 94103 and (415) 374-7782. We will not, however, send exhibits to those documents, unless the exhibits are specifically incorporated by reference in those documents.

We make available free of charge on our website our annual reports on Form 10-K, quarterly reports on Form 10-Q, current reports on Form 8-K and amendments to those reports, as soon as reasonably practicable after we electronically file or furnish such materials to the SEC. You may also obtain a free copy of these reports in the Investor Relations section of our website, www.invitae.com.

PART II

Information Not Required In Prospectus

The following is a statement of estimated expenses in connection with the issuance and distribution of the securities being registered, other than brokerage or underwriting discounts and commissions.registered. All expenses and all brokerage or underwriting discounts and commissions will be paid byof the selling stockholders.amounts are estimated except the SEC registration fee.

Section 102 of the Delaware General Corporation Law, (the “DGCL”)or the DGCL, allows a corporation to eliminate the personal liability of directors of a corporation to the corporation or its stockholders for monetary damages for breach of fiduciary duty as a director, except where the director breached the duty of loyalty, failed to act in good faith, engaged in intentional misconduct or knowingly violated a law, authorized the payment of a dividend or approved a stock repurchase in violation of the DGCL or obtained an improper personal benefit.

Section 145 of the DGCL provides, among other things, that we may indemnify any person who was or is a party or is threatened to be made a party to any threatened, pending or completed action, suit or proceeding, proceeding—other than an action by or in the right of the Registrant, Registrant—by reason of the fact that the person is or was a director, officer, agent or employee of the Registrant, or is or was serving at our request as a director, officer, agent or employee of another corporation, partnership, joint venture, trust or other enterprise against expenses, including attorneys’ fees, judgments, fines and amounts paid in settlement actually and reasonably incurred by the person in connection with such action, suit or proceeding. The power to indemnify applies (a) if such person is successful on the merits or otherwise in defense of any action, suit or proceeding, or (b) if such person acting in good faith and in a manner he or she reasonably believed to be in the best interest, or not opposed to the best interest, of the Registrant, and with respect to any criminal action or proceeding had no reasonable cause to believe his or her conduct was unlawful. The power to indemnify applies to actions brought by or in the right of the Registrant as well but only to the extent of defense expenses, including attorneys’ fees but excluding amounts paid in settlement, actually and reasonably incurred and not to any satisfaction of judgment or settlement of the claim itself, and with the further limitation that in such actions no indemnification shall be made in the event of any adjudication of liability to the Registrant, unless the court believes that in light of all the circumstances indemnification should apply.

Section 174 of the DGCL provides, among other things, that a director, who willfully or negligently approves of an unlawful payment of dividends or an unlawful stock purchase or redemption, may be held liable for such actions. A director who was either absent when the unlawful actions were approved or dissented at the time, may avoid liability by causing his or her dissent to such actions to be entered in the books containing minutes of the meetings of the board of directors at the time such action occurred or immediately after such absent director receives notice of the unlawful acts.

The Registrant’s restated certificate of incorporation, filed as Exhibit 3.1 to the Registrant’s Current Report on Form 8-K filed on February 23, 2015 and the Registrant’s amended and restated bylaws, filed as ExhibitsExhibit 3.1 and 3.2 to the Registrant’Registrant’s Current Report on Form 8-K filed on February 22, 2015,March 23, 2021, provide that the Registrant

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shall indemnify its directors, officers, employees and other agents to the fullest extent not prohibited by the DGCL or any other applicable law. In addition, the Registrant has entered into agreements withto indemnify its directors and officers thatexpects to continue to enter into agreements to indemnify all of its directors. These agreements require the

Registrant, among other things, to indemnify theits directors and officers against certain liabilities thatwhich may arise by reason of their status or service as directors or officers to the fullest extent not prohibited by law. These indemnification provisions and the indemnification agreements may be sufficiently broad to permit indemnification of the Registrant’s officers and directors for liabilities, including reimbursement of expenses incurred, arising under the Securities Act of 1933, as amended. The Registrant also intends to maintain director and officer liability insurance, if available on reasonable terms.Act.

The list of exhibits in the Exhibit Index to this registration statement is incorporated herein by reference.

(a) The undersigned Registrantregistrant hereby undertakes:

(1) To file, during any period in which offers or sales are being made, a post-effective amendment to this registration statement:

(i) To include any prospectus required by Section 10(a)(3) of the Securities Act of 1933;Act;

(ii) To reflect in the prospectus any facts or events arising after the effective date of the registration statement (or the most recent post-effective amendment thereof) which, individually or in the aggregate, represent a fundamental change in the information set forth in the registration statement. Notwithstanding the foregoing, any increase or decrease in volume of securities offered (if the total dollar value of securities offered would not exceed that which was registered) and any deviation from the low or high end of the estimated maximum offering range may be reflected in the form of

prospectus filed with the Securities and Exchange CommissionSEC pursuant to Rule 424(b) if, in the aggregate, the changes in volume and price represent no more than a 20 percent change in the maximum aggregate offering price set forth in the “Calculation of Registration Fee” table in the effective registration statement; and

(iii) To include any material information with respect to the plan of distribution not previously disclosed in the registration statement or any material change to such information in the registration statement;

provided, however,, that paragraphs (i), (ii) and (iii) above do not apply if the information required to be included in a post-effective amendment by those paragraphs is contained in reports filed with or furnished to the Securities and Exchange CommissionSEC by the Registrantregistrant pursuant to Sectionsection 13 or Sectionsection 15(d) of the Securities Exchange Act of 1934 that are incorporated by reference in the registration statement, or is contained in a form of prospectus filed pursuant to Rule 424(b) that is part of the registration statement.

(2) That, for the purpose of determining any liability under the Securities Act, of 1933, each such post-effective amendment shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

(3) To remove from registration by means of a post-effective amendment any of the securities being registered which remain unsold at the termination of the offering.

(4) That, for the purpose of determining liability under the Securities Act of 1933 to any purchaser:

(A) Each prospectus filed by the registrant pursuant to Rule 424(b)(3) shall be deemed to be part of the registration statement as of the date the filed prospectus was deemed part of and included in the registration statement; and

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(B) Each prospectus required to be filed pursuant to Rule 424(b)(2), (b)(5), or (b)(7) as part of a registration statement in reliance on Rule 430B relating to an offering made pursuant to Rule 415(a)(1)(i), (vii), or (x) for the purpose of providing the information required by Sectionsection 10(a) of the Securities Act of 1933 shall be deemed to be part of and included in the registration statement as of the earlier of the date such form of prospectus is first used after effectiveness or the date of the first contract of sale of securities in the offering described in the prospectus. As provided in Rule 430B, for liability purposes of the issuer and any person that is at that date an underwriter, such date shall be deemed to be a new effective date of the registration statement relating to the securities in the registration statement to which that prospectus relates, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.Provided, however,, that no statement made in a registration statement or prospectus that is part of the registration statement or made in a document incorporated or deemed incorporated by reference into the registration statement or prospectus that is part of the registration statement will, as to a purchaser with a time of contract of sale prior to such effective date, supersede or modify any statement that was made in the registration statement or prospectus that was part of the registration statement or made in any such document immediately prior to such effective date.

(5) That, for the purpose of determining liability of the registrant under the Securities Act to any purchaser in the initial distribution of the securities: The undersigned registrant undertakes that in a primary offering of securities of the undersigned registrant pursuant to this registration statement, regardless of the underwriting method used to sell the securities to the purchaser, if the securities are offered or sold to such purchaser by means of any of the following communications, the undersigned registrant will be a seller to the purchaser and will be considered to offer or sell such securities to such purchaser:

(i) Any preliminary prospectus or prospectus of the undersigned registrant relating to the offering required to be filed pursuant to Rule 424;

(ii) Any free writing prospectus relating to the offering prepared by or on behalf of the undersigned registrant or used or referred to by the undersigned registrant;

(iii) The portion of any other free writing prospectus relating to the offering containing material information about the undersigned registrant or its securities provided by or on behalf of the undersigned registrant; and

(iv) Any other communication that is an offer in the offering made by the undersigned registrant to the purchaser.

(b) The undersigned registrant hereby undertakes that, for purposes of determining any liability under the Securities Act, of 1933, each filing of the Registrant’sregistrant’s annual report pursuant to Section 13(a) or Section 15(d) of the Securities Exchange Act of 1934 (and, where applicable, each filing of an employee benefit plan’s annual report pursuant to Section 15(d) of the Securities Exchange Act of 1934)Act) that is incorporated by reference in the registration statement shall be deemed to be a new registration statement relating to the securities offered therein, and the offering of such securities at that time shall be deemed to be the initial bona fide offering thereof.

Insofar as indemnification for liabilities arising under the Securities Act of 1933 may be permitted to directors, officers and controlling persons of the Registrant pursuant to any charter provision, by law or otherwise, the Registrant has been advised that in the opinion of the Securities and Exchange Commission such indemnification is against public policy as expressed in the Securities Act of 1933 and is, therefore, unenforceable. In the event that a claim for indemnification against such liabilities (other than payment by the Registrant of expenses incurred or paid by a director, officer or controlling person of the Registrant in the successful defense of any action, suit or proceeding) is asserted by such director, officer or controlling person in connection with the securities being registered, the Registrant will, unless in the opinion of its counsel the matter has been settled by controlling precedent, submit to a court of appropriate jurisdiction the question whether such indemnification by it is against public policy as expressed in the Securities Act and will be governed by the final adjudication of such issue.

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SIGNATURES

Pursuant to the requirements of the Securities Act of 1933, the Registrant certifies that it has reasonable grounds to believe that it meets all of the requirements for filing on Form S-3 and has duly caused this Registration Statement to be signed on its behalf by the undersigned, thereunto duly authorized in the City of San Francisco, State of California, on August 18, 2017.March 17, 2023.

POWER OF ATTORNEY

KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature appears below hereby constitutes and appoints Sean E. George, Ph.D., ShellyKenneth D. GuyerKnight and Patricia E. Dumond,Yafei (Roxi) Wen, and each of them, his or her true and lawfulattorneys-in-fact and agents, with full power of substitution and resubstitution, for him or her and in his or her name, place and stead, in any and all capacities, to sign any and all amendments, including post-effective amendments, to this Registration Statement, and any registration statement relating to the offering covered by this Registration Statement and filed pursuant to Rule 462(b) under the Securities Act of 1933, and to file the same, with exhibits thereto and other documents in connection therewith, with the Securities and Exchange Commission, granting unto said attorneys-in-fact and agents, and each of them, full power and authority to do and perform each and every act and thing requisite and necessary to be done, as fully for all intents and purposes as he or she might or could do in person, hereby ratifying and confirming all that each of said attorneys in fact and agents or their substitute or substitutes may lawfully do or cause to be done by virtue hereof.

Pursuant to the requirements of the Securities Act of 1933, this Registration Statement has been signed by the following persons in the capacities and on the dates indicated.

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EXHIBIT INDEX