[SCHEDULE 13D/A] Prime Medicine, Inc. SEC Filing

Rhea-AI Filing Summary

ARCH Venture group and certain affiliated funds and individuals report collective beneficial ownership of 18,486,894 shares of Prime Medicine common stock, representing 10.4% of the outstanding class on the basis described in this filing. The disclosure aggregates holdings across multiple ARCH entities and related partnerships and shows shared voting and dispositive power over those shares.

The filing also discloses that AVF XII purchased 3,030,300 shares at $3.30 per share in a public offering, for total consideration of $9,999,990, funded from AVF XII working capital. The amendment was filed because an issuer offering (an August 2025 issuance of 43,700,000 shares) changed the Reporting Persons' percentage ownership by one percent or more. The statement notes existing registration rights under an Amended and Restated Investors' Rights Agreement and that no Reporting Person was subject to disqualifying legal proceedings in the prior five years.

Positive

• Significant disclosed stake: ARCH entities report beneficial ownership of 18,486,894 shares (10.4%) of Prime Medicine common stock
• Recent meaningful purchase: AVF XII acquired 3,030,300 shares at $3.30 per share, totaling $9,999,990, funded by working capital
• Registration rights: Reporting Persons reference an Amended and Restated Investors' Rights Agreement that provides demand, piggyback and Form S-3 registration rights

Negative

• Dilution of ownership percentage: The Reporting Persons' percentage ownership declined by ≥1% due to an issuer offering of 43,700,000 shares reported by the issuer
• Shared control: Reported holdings show shared voting and dispositive power rather than sole control, which may limit unilateral influence

Insights

Financial Analyst

TL;DR: ARCH-affiliated funds report a material ~10.4% stake in Prime Medicine and a $10.0M open-market purchase at $3.30 per share.

The filing documents concentrated ownership across multiple ARCH funds totaling 18,486,894 shares with shared voting and dispositive power, and an additional disclosure that AVF XII paid $9,999,990 for 3,030,300 shares. These facts are material for shareholders because they quantify a sizeable passive position and a recent capital outlay by an affiliated fund. The amendment was triggered by an issuer share issuance that altered ownership percentages, and the filing confirms registration rights that may affect future sales of these shares.

Corporate Governance Expert

TL;DR: Multiple ARCH entities and named committee members report shared control over a >10% block and disclose investor rights; no legal encumbrances reported.

The filing shows a coordinated group of ARCH funds and committee members with shared voting/dispositive power over the reported shares, which is significant under governance rules because ownership at this scale can affect proxy dynamics. The Investors' Rights Agreement cited preserves registration rights for these holders. The filing also discloses that none of the Reporting Persons were subject to recent criminal or civil securities judgments, which is relevant to governance risk assessments.

SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

SCHEDULE 13D

Under the Securities Exchange Act of 1934

(Amendment No. 2)

Prime Medicine, Inc.

(Name of Issuer)

Common Stock, $0.00001 par value

(Title of Class of Securities)

74168J101

(CUSIP Number)

Mark McDonnell
ARCH Venture Management, LLC, 8755 W. Higgins Road Suite 1025
Chicago, IL, 60631
(773)380-6600

(Name, Address and Telephone Number of Person Authorized to Receive Notices and Communications)

08/07/2025

(Date of Event Which Requires Filing of This Statement)

If the filing person has previously filed a statement on Schedule 13G to report the acquisition that is the subject of this Schedule 13D, and is filing this schedule because of §§ 240.13d-1(e), 240.13d-1(f) or 240.13d-1(g), check the following box.

The information required on the remainder of this cover page shall not be deemed to be "filed" for the purpose of Section 18 of the Securities Exchange Act of 1934 ("Act") or otherwise subject to the liabilities of that section of the Act but shall be subject to all other provisions of the Act (however, see the Notes).

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Fund X, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

WC

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Fund X Overage, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

WC

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Fund XII, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

WC

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Partners X, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Partners X Overage, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Partners XII, L.P.

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

WC

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

PN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Partners X, LLC

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

OO

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

ARCH Venture Partners XII, LLC

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

DELAWARE

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

OO

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

Robert Nelsen

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 100,142.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 100,142.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,587,036.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

IN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

Keith Crandell

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

IN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

Kristina Burow

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

IN

SCHEDULE 13D

CUSIP No. 74168J101

1

Name of reporting person

Steven Gillis

2

Check the appropriate box if a member of a Group (See Instructions)

(a)
(b)

3

SEC use only

4

Source of funds (See Instructions)

AF

5

Check if disclosure of legal proceedings is required pursuant to Items 2(d) or 2(e)

6

Citizenship or place of organization

UNITED STATES

Number of Shares Beneficially Owned by Each Reporting Person With:

7	Sole Voting Power 0.00
8	Shared Voting Power 18,486,894.00
9	Sole Dispositive Power 0.00
10	Shared Dispositive Power 18,486,894.00

11

Aggregate amount beneficially owned by each reporting person

18,486,894.00

12

Check if the aggregate amount in Row (11) excludes certain shares (See Instructions)

13

Percent of class represented by amount in Row (11)

10.4 %

14

Type of Reporting Person (See Instructions)

IN

SCHEDULE 13D

Item 1.	Security and Issuer
(a)	Title of Class of Securities: Common Stock, $0.00001 par value
(b)	Name of Issuer: Prime Medicine, Inc.
(c)	Address of Issuer's Principal Executive Offices: 21 Erie Street, Cambridge, MASSACHUSETTS , 02139.
Item 1 Comment: This statement relates to the Common Stock, $0.00001 par value per share (the "Common Stock"), of Prime Medicine, Inc. (the "Issuer") having its principal executive office at 21 Erie St., Cambridge, MA 02139 USA.
Item 2.	Identity and Background
(a)	This statement is being filed by (1) ARCH Venture Fund X, L.P. ("AVF X"), (2) ARCH Venture Partners X, L.P. ("AVP X LP") which is the sole general partner of AVF X, (3) ARCH Venture Partners X, LLC ("AVP X LLC") which is the sole general partner of AVP X LP and AVP X Overage LP (defined below), (4) ARCH Venture Fund X Overage, L.P. ("AVF X Overage"), (5) ARCH Venture Partners X Overage, L.P. ("AVP X Overage LP"), which is the sole general partner of AVF X Overage, (6) ARCH Venture Fund XII, L.P. ("AVF XII"), (7) ARCH Venture Partners XII, L.P. ("AVP XII LP") which is the sole general partner of AVF XII, (8) ARCH Venture Partners XII, LLC ("AVP XII LLC") which is the sole general partner of AVP XII LP, (9) Keith Crandell ("Crandell"), (10) Robert Nelsen ("Nelsen"), (11) Kristina Burow ("Burow"), and (12) Steven Gillis ("Gillis", and together with Nelsen, Crandell and Burow, referred to individually as "Committee Member" or collectively as either the "AVP X Investment Committee Members" or the "AVP XII Investment Committee Members"). Each of the individuals and entities above shall be referred to herein as a "Reporting Person" and collectively as the "Reporting Persons".
(b)	The business address of each of the Reporting Persons is 8755 West Higgins Road, Suite 1025, Chicago, IL, 60631.
(c)	The principal business of AVP X LP is to act as the general partner of AVF X, the principal business of AVP X Overage LP is to act as the general partner of AVF X Overage, and the principal business of AVP XII is to act as the general partner of AVF XII. The principal business of AVP X LLC is to act as the general partner of AVP X LP and AVF X Overage LP, and the principal business of AVP XII LLC is to act as the general partner of AVP XII LP. AVP X Investment Committee Members and AVP XII Investment Committee Members act as investment committee members of AVP X LLC and AVP XII LLC, respectively, and as managing directors or investment committee members of a number of affiliated partnerships with similar businesses.
(d)	During the five years prior to the date hereof, none of the Reporting Persons has been convicted in a criminal proceeding.
(e)	During the five years prior to the date hereof, none of the Reporting Persons has been a party to a civil proceeding of a judicial or administrative body of competent jurisdiction ending in a judgment, decree or 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.
(f)	Each of AVF X, AVP X LP, AVF X Overage, AVP X Overage LP, AVF XII and AVP XII LP, are limited partnerships organized under the laws of the State of Delaware. Each of AVP X LLC and AVP XII LLC is a limited liability company organized under the laws of the State of Delaware. Each Committee Member is a US citizen.
Item 5.	Interest in Securities of the Issuer
(a)	AVF X is the record owner of 6,128,297 shares of Common Stock ("AVF X Record Shares"). AVP X LP, as the sole general partner of AVF X LP, may be deemed to beneficially own the AVF X Record Shares. AVP X LLC, as the sole general partner of AVP X LP, may be deemed to beneficially own the AVF X Record Shares. AVF X Overage is the record holder of 6,128,297 shares of Common Stock ("AVF X Overage Record Shares"). AVP X Overage LP, as the sole general partner of AVF X Overage, may be deemed to beneficially own the AVF X Overage Record Shares. AVP X LLC, as the sole general partner of AVP X Overage LP, may be deemed to beneficially own the AVF X Overage Record Shares. AVF XII is the record holder of 6,230,300 shares of Common Stock ("AVF XII Record Shares"). AVP XII LP, as the sole general partner of AVF XII LP, may be deemed to beneficially own the AVF XII Record Shares. AVP XII LLC, as the sole general partner of AVP XII LP, may be deemed to beneficially own the AVF XII Overage Record Shares. By virtue of their relationship as affiliated entities who have overlapping general partners and investment committee members, each of the Committee Members and direct and indirect general partners of AVF X, AVF X Overage and AVF XII may be deemed to share the power to direct AVF X Record Shares, AVF Overage X Record Shares and AVF XII Record Shares (collectively the "Record Shares"). Nelsen and his related trusts are also the owner of 16,080 shares of Common Stock of the Issuer and is the holder of vested options to purchase 84,062 shares of Common Stock ("Nelsen Options"). Each Reporting Person disclaims beneficial ownership of the Record Shares except for the shares, if any, held of record by such Reporting Person. The percentage of outstanding Common Stock of the Issuer which may be deemed to be beneficially owned by each Reporting Person (other than Nelsen) is set forth on Line 13 of such Reporting Person's cover sheet. Such percentage was calculated based on the 134,573,998 shares of Common Stock reported by the Issuer to be outstanding on July 31, 2025 in the Issuer's Form 10-Q filed with the Securities and Exchange Commission on August 7, 2025, plus 43,700,000 shares sold in an offering in August 2025. For Nelsen, the Nelsen Options were included in the number of shares of Common Stock outstanding.
(b)	Regarding the number of shares as to which such person has: (i) sole power to vote or to direct the vote: See line 7 of cover sheets. (ii) shared power to vote or to direct the vote: See line 8 of cover sheets. (iii) sole power to dispose or to direct the disposition: See line 9 of cover sheets. (iv) shared power to dispose or to direct the disposition: See line 10 of cover sheets.
(c)	On August 1, 2025, AVF XII purchased 3,030,300 shares of Common Stock at purchase price of $3.30 in a public offering. The working capital of AVF XII was the source of the funds for the purchase. No part of the purchase price paid by AVF XII was represented by funds or other consideration borrowed or otherwise obtained for the purpose of acquiring, holding, trading or voting the shares of Common Stock described above. The total amount paid by for securities purchased in the above-listed transactions is as follows: AVF XII: $ 9,999,990.00 This Amendment No. 2 is being filed voluntarily due to an issuance of securities by the Issuer as reported on the Issuer's 10-Q filed with the Securities and Exchange Commission on August 7, 2025, which caused the percentage of outstanding Common Stock of the Issuer deemed to be beneficial owned by the Reporting Persons to reduce by one percent or more.
(d)	No other person is known to have the right to receive or the power to direct the receipt of dividends from, or any proceeds from the sale of, shares beneficially owned by any of the Reporting Persons.
(e)	Not applicable
Item 6.	Contracts, Arrangements, Understandings or Relationships With Respect to Securities of the Issuer
	AVF X and AVF X Overage are parties to that certain Amended and Restated Investors' Rights Agreement, dated April 20, 2021, the "Investor Rights Agreement"), which is attached as Exhibit 4.1+ to the Issuer's Form S-1 filed on September 23, 2022. Effective as of the closing of the Issuer's initial public offering, the covenants relating to delivery of financial statements and inspection rights set forth in Section 3 were terminated and rights of first offer were terminated. Pursuant to the Investor Rights Agreement, AVF X and AVF X Overage have certain registration rights with respect to its Common Stock. Specifically, the Issuer has granted demand, piggyback and Form S-3 registration rights, which will terminate upon the earlier of (i) with respect to each stockholder, such date on which all registrable shares held by such stockholder may immediately be sold during any three-month period pursuant to Rule 144 of the Securities Act of 1933, as amended, (ii) the occurrence of a deemed liquidation event, as defined in the Issuer's amended and restated certificate of incorporation, as currently in effect, and (iii) the fifth anniversary of the IPO. The foregoing description of the Investor Rights Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of such agreement filed as an exhibit to this Schedule 13D and is incorporated herein by reference.
Item 7.	Material to be Filed as Exhibits.
	Exhibit 1- Agreement of Joint Filing Exhibit 2- Agreement of Joint Filing Exhibit 3- Amended and Restated Investors' Rights Agreement, dated April 20, 2021, as amended, by and among the Issuer and certain of its stockholders (incorporated by reference to Exhibit 4.1+ to the Issuer's Registration Statement on Form S-1 (File No.), as filed with the Securities and Exchange Commission on September 23, 2022)

SIGNATURE

After reasonable inquiry and to the best of my knowledge and belief, I certify that the information set forth in this statement is true, complete and correct.

ARCH Venture Fund X, L.P.

Signature:	ARCH Venture Partners X, L.P.
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	ARCH Venture Partners X, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Robert Nelsen, Managing Director
Date:	08/11/2025

ARCH Venture Fund X Overage, L.P.

Signature:	ARCH Venture Partners X Overage, L.P.
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	ARCH Venture Partners X, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director
Date:	08/11/2025

ARCH Venture Fund XII, L.P.

Signature:	ARCH Venture Partners XII, L.P.
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	ARCH Venture Partners XII, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director
Date:	08/11/2025

ARCH Venture Partners X, L.P.

Signature:	ARCH Venture Partners X, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Robert Nelsen, Managing Director
Date:	08/11/2025

ARCH Venture Partners X Overage, L.P.

Signature:	ARCH Venture Partners X, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director
Date:	08/11/2025

ARCH Venture Partners XII, L.P.

Signature:	ARCH Venture Partners XII, LLC
Name/Title:	its General Partner
Date:	08/11/2025

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director
Date:	08/11/2025

ARCH Venture Partners X, LLC

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Robert Nelsen, Managing Director
Date:	08/11/2025

ARCH Venture Partners XII, LLC

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell, Managing Director
Date:	08/11/2025

Robert Nelsen

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Robert Nelsen
Date:	08/11/2025

Keith Crandell

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Keith Crandell
Date:	08/11/2025

Kristina Burow

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Kristina Burow
Date:	08/11/2025

Steven Gillis

Signature:	/s/ Mark McDonnell
Name/Title:	Mark McDonnell, as Attorney-in-Fact for Steven Gillis
Date:	08/11/2025

Comments accompanying signature:

*This Schedule 13D was executed by Mark McDonnell pursuant to Powers of Attorney filed as Exhibit 24 and 24.1 to the Form 3 relating to the beneficial ownership of shares of Prime Medicine, Inc. by the Reporting Persons filed with the Securities Exchange Commission on October 19, 2022 and pursuant to a Power of Attorney filed as Exhibit 24.4 to the Form 3 relating to the beneficial ownership of shares by the Reporting Persons of Neumora Therapeutics, Inc. filed with the Securities Exchange Commission on September 14, 2023 and incorporated herein in its entirety by reference.

FAQ

How many Prime Medicine (PRME) shares do ARCH entities report owning?

The ARCH reporting persons disclose beneficial ownership of 18,486,894 shares, representing 10.4% of the outstanding class as calculated in the filing.

Did any ARCH fund recently buy additional PRME shares and what was the cost?

Yes. AVF XII purchased 3,030,300 shares at $3.30 per share on August 1, 2025, for a total of $9,999,990, funded from working capital.

Why was Amendment No. 2 filed for this Schedule 13D/A?

The amendment was filed because the issuer completed an offering (the filing cites 43,700,000 shares sold in August 2025) that caused the Reporting Persons' percentage ownership to decrease by one percent or more.

Do the Reporting Persons have registration rights for their PRME shares?

Yes. AVF X and AVF X Overage are party to an Amended and Restated Investors' Rights Agreement that grants demand, piggyback and Form S-3 registration rights as described in the filing.

Are any of the Reporting Persons subject to recent legal or criminal judgments related to securities laws?

No. The filing states that during the prior five years none of the Reporting Persons was convicted in a criminal proceeding or was a party to a civil proceeding ending in specified securities-related judgments.