SCHEDULE 13G 0001346824 XXXXXXXX LIVE Class A Common Stock, $0.0001 par value per share 10/23/2025 0001856725 RANI THERAPEUTICS HOLDINGS, INC. 753018100 2051 RINGWOOD AVENUE SAN JOSE CA 95131 Rule 13d-1(c) RA Capital Management, L.P. DE 0.00 9882477.00 0.00 9882477.00 9882477.00 9.9 IA PN Peter Kolchinsky X1 0.00 9882477.00 0.00 9882477.00 9882477.00 9.9 HC IN Rajeev Shah X1 0.00 9882477.00 0.00 9882477.00 9882477.00 9.9 HC IN RA Capital Healthcare Fund, L.P. DE 0.00 9882477.00 0.00 9882477.00 9882477.00 9.9 PN RANI THERAPEUTICS HOLDINGS, INC. 2051 RINGWOOD AVENUE, SAN JOSE, CA, 95131. The names of the persons filing this report (collectively, the "Reporting Persons") are: RA Capital Management, L.P. ("RA Capital") Peter Kolchinsky ("Dr. Kolchinsky") Rajeev Shah ("Mr. Shah") RA Capital Healthcare Fund, L.P. (the "Fund") The Reporting Persons expressly disclaim status as a "group" for purposes of this Schedule 13G. The address of the principal business office of each of the Reporting Persons is: c/o RA Capital Management, L.P., 200 Berkeley Street, 18th Floor, Boston MA 02116 RA Capital and the Fund are Delaware limited partnerships. Dr. Kolchinsky and Mr. Shah are United States citizens. Y Row 9 of each Reporting Person's cover page to this Schedule 13G sets forth the aggregate number of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. The Fund directly holds (i) 8,500,000 shares of Class A common stock; (ii) pre-funded warrants (the "Pre-Funded Warrants") exercisable for up to 16,500,000 shares of Class A common stock; and (iii) warrants (the "Common Warrants" and, together with the Pre-Funded Warrants, the "Warrants") exercisable for up to 25,000,000 shares of Class A common stock. Each of the Pre-Funded Warrants and the Common Warrants contains a provision (the "Beneficial Ownership Blockers") which precludes exercise of the Warrants to the extent that, following exercise, the Fund, together with its affiliates and other attribution parties, would own more than 9.99% of the Class A common stock outstanding. Additionally, the Common Warrants are not exercisable until the effective date of the approval by the Issuer's stockholders of such exercisability, in accordance with the rules of the Nasdaq Stock Market. The Fund is currently prohibited from exercising the Warrants to the extent that such exercise would result in the Reporting Persons' beneficial ownership of more than 9,882,477 shares of Class A common stock. RA Capital Healthcare Fund GP, LLC is the general partner of the Fund. 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 the Fund and may be deemed a beneficial owner, for purposes of Section 13(d) of the Act, of any securities of the Issuer held by the Fund. The Fund has delegated to RA Capital the sole power to vote and the sole power to dispose of all securities held in the Fund's portfolio, including the shares of the Issuer's Class A common stock reported herein. Because the Fund has divested voting and investment power over the reported securities it holds and may not revoke that delegation on less than 61 days' notice, the Fund disclaims beneficial ownership of the securities it holds for purposes of 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 Schedule 13G other than for the purpose of determining their obligations under Section 13(d) of the Act, and the filing of this Schedule 13G 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. Due to the Beneficial Ownership Blockers listed in the Warrants, each Reporting Person's beneficial ownership percentage is 9.99%. Such percentage is based upon the sum of (i) 97,541,221 shares of Class A common stock outstanding as of October 23, 2025, as reported in the Issuer's Current Report on Form 8-K filed with the Securities and Exchange Commission (the "SEC") on October 27, 2025 and (ii) 1,382,477 shares of Class A common stock issuable upon the exercise of Warrants. Due to field limitations of the EDGAR filing system, the percentages listed in Row 11 of the Reporting Persons' cover pages have been rounded down to 9.9%. Row 5 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 6 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to vote or to direct the vote of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 7 of each Reporting Person's cover page to this Schedule 13G sets forth the sole power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Row 8 of each Reporting Person's cover page to this Schedule 13G sets forth the shared power to dispose or to direct the disposition of securities of the Issuer beneficially owned by such Reporting Person and is incorporated by reference. Y Y Y Y Y N By signing below I certify that, to the best of my knowledge and belief, the securities referred to above were not acquired and are not held for the purpose of or with the effect of changing or influencing the control of the issuer of the securities and were not acquired and are not held in connection with or as a participant in any transaction having that purpose or effect, other than activities solely in connection with a nomination under ?? 240.14a-11. Exhibit 99.1 Joint Filing Agreement RA Capital Management, L.P. /s/ Peter Kolchinsky 10/30/2025 Peter Kolchinsky /s/ Peter Kolchinsky 10/30/2025 Rajeev Shah /s/ Rajeev Shah 10/30/2025 RA Capital Healthcare Fund, L.P. /s/ Peter Kolchinsky 10/30/2025