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SCHEDULE 13D/A 0001104659-24-040539 0001346824 XXXXXXXX LIVE 1 Common Stock, $0.00001 par value per share 05/07/2025 false 0001815776 52635N103 LENZ THERAPEUTICS, INC. 445 Marine View Ave., Ste. #320 Del Mar CA 92014 Peter Kolchinsky 617.778.2500 RA Capital Management, L.P. 200 Berkeley Street, 18th Floor Boston MA 02116 0001346824 N RA Capital Management, L.P. AF N DE 0.00 4260606.00 0.00 4260606.00 4260606.00 N 15.1 IA PN 0001384859 N Peter Kolchinsky AF N X1 0.00 4260606.00 0.00 4260606.00 4260606.00 N 15.1 HC IN 0001619841 N Rajeev Shah AF N X1 0.00 4260606.00 0.00 4260606.00 4260606.00 N 15.1 HC IN 0001315082 N RA Capital Healthcare Fund, L.P. WC N DE 0.00 3373921.00 0.00 3373921.00 3373921.00 N 12.0 PN Common Stock, $0.00001 par value per share LENZ THERAPEUTICS, INC. 445 Marine View Ave., Ste. #320 Del Mar CA 92014 Item 1 of the Statement is amended and supplemented as follows: This Amendment No. 1 (this "Amendment No. 1" or this "13D/A") amends and supplements the statement on Schedule 13D originally filed with the Securities and Exchange Commission (the "SEC") on March 28, 2024 (the "Statement") by the Reporting Persons. Unless otherwise defined herein, capitalized terms used in this Amendment No. 1 shall have the meanings ascribed to them in the Statement. Unless amended or supplemented below, the information in the Statement remains unchanged. This Amendment No. 1 is being filed on behalf of RA Capital Management, L.P. ("RA Capital"), Peter Kolchinsky, Rajeev Shah, and RA Capital Healthcare Fund, L.P. (the "Fund"), who are collectively referred to herein as the "Reporting Persons." The agreement among the Reporting Persons to file this 13D/A jointly in accordance with Rule 13d-1(k) of the Securities Exchange Act of 1934, as amended (the "Act"), is attached hereto as Exhibit 99.1. The Reporting Persons' beneficial ownership of the Issuer's Common Stock consists of (i) 3,319,339 shares of Common Stock and 54,582 shares of common stock issuable upon the exercise of immediately exercisable warrants ("Warrants") directly held by the Fund; (ii) 694,755 shares of common stock and 10,580 shares of common stock issuable upon the exercise of immediately exercisable Warrants directly held by the RA Capital Nexus Fund II, L.P (the "Nexus Fund II"); (iii) 164,729 shares of common stock and 5,371 shares of common stock issuable upon the exercise of immediately exercisable Warrants directly held by a separately managed account (the "Account"); (iv) 9,750 vested stock options (right to buy) and 1,500 stock options (right to buy) scheduled to vest within 60 days of this filing held by Dr. Zach Scheiner for the benefit of RA Capital. RA Capital Healthcare Fund GP, LLC is the general partner of the Fund and RA Capital Nexus Fund II GP, LLC is the general partner of the Nexus Fund II. The general partner of RA Capital is RA Capital Management GP, LLC, of which Dr. Kolchinsky and Mr. Shah are the controlling persons. RA Capital serves as investment adviser for each of the Fund, the Nexus Fund II and the Account and may be deemed a beneficial owner, for purposes of Section 13(d) of the Securities Exchange Act of 1934 (the "Act"), of any securities of the Issuer held by the Fund, the Nexus Fund II or the Account. Each of the Fund and the Nexus Fund II has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in its portfolio, including the shares of the Issuer's Common Stock reported herein. Because each of the Fund and the Nexus Fund II has divested itself of voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, each of the Fund and the Nexus Fund II disclaims beneficial ownership of the securities it holds for purposes of Section 13(d) of the Act and therefore disclaims any obligation to report ownership of the reported securities under Section 13(d) of the Act. As managers of RA Capital, Dr. Kolchinsky and Mr. Shah may be deemed beneficial owners, for purposes of Section 13(d) of the Act, of any securities of the Issuer beneficially owned by RA Capital. RA Capital, Dr. Kolchinsky, and Mr. Shah disclaim beneficial ownership of the securities reported in this 13D/A other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this 13D/A shall not be deemed an admission that either RA Capital, Dr. Kolchinsky, or Mr. Shah is the beneficial owner of such securities for any other purpose. The address of the principal business office of each of the Reporting Persons is 200 Berkeley Street, 18th Floor, Boston, MA 02116. The Fund is a private investment vehicle. RA Capital provides investment management services to the Fund, the Nexus Fund II and the Account. The principal occupation of each of Dr. Kolchinsky and Mr. Shah is investment management. During the last five years, none of the Reporting Persons has been convicted in a criminal proceeding (excluding traffic violations or similar misdemeanors). During the last five years, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction and as a result of such proceeding was or is subject to a judgment, decree of final order enjoining future violations of, or prohibiting or mandating activities subject to, federal or state securities laws or finding any violation with respect to such laws. See Item 6 of the cover pages. Rows 11 and 13 of each Reporting Person's cover page to this 13D/A set forth the aggregate number of shares of common stock and percentages of the shares of common stock beneficially owned by such Reporting Person and are incorporated by reference. The percentage set forth in each row 13 is based upon 28,146,154 shares of common stock outstanding as of May 1, 2025, as reported in the Issuer's quarterly Report on Form 10-Q filed with the SEC on May 7, 2025, and giving effect to stock options and Warrants, to the extent exercisable within 60 days hereof, as referenced herein. Rows 7 through 10 of each Reporting Person's cover page to this 13D/A set forth the number of shares of common stock as to which such Reporting Person has the sole or shared power to vote or direct the vote and sole or shared power to dispose or to direct the disposition and are incorporated by reference. Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer during the past sixty days: No. Price Per Transaction Purchaser Date Shares Share Vest Stock Option (Right to Buy) RA Capital 03/21/2025 750 (1) Vest Stock Option (Right to Buy) RA Capital 04/21/2025 750 (1) Vest Stock Option (Right to Buy) RA Capital 05/21/2025 750 (1)(2) Vest Stock Option (Right to Buy) RA Capital 06/21/2025 750 (1)(2) (1) This option represents a right to purchase a total of 27,000 shares of the Issuer's Common Stock, which vests from March 21, 2024 in 36 equal monthly installments over three years, subject to Dr. Scheiner's continued service to the Issuer through each vesting date. These options have an exercise price of $15.05 per share. (2) Represents future vesting options within 60 days from the filing date of this Amendment No. 1. Except as set forth below, none of the Reporting Persons has effected any transactions with respect to the securities of the Issuer since the most recent amendment to this 13D/A. Not applicable. Exhibit 99.1 Joint Filing Agreement RA Capital Management, L.P. /s/ Peter Kolchinsky By Peter Kolchinsky, Authorized Signatory 05/09/2025 Peter Kolchinsky /s/ Peter Kolchinsky Peter Kolchinsky 05/09/2025 Rajeev Shah /s/ Rajeev Shah Rajeev Shah 05/09/2025 RA Capital Healthcare Fund, L.P. /s/ Peter Kolchinsky By RA Capital Healthcare Fund GP, LLC, its General Partner, By Peter Kolchinsky, Manager 05/09/2025