Stoke Therapeutics, Inc.

Issuer

Stoke Therapeutics, Inc.

Principal executive office address

45 WIGGINS AVENUE, BEDFORD, MA 01730

Citizenship

Biotechnology Value Fund, L.P. Delaware BVF I GP LLC Delaware Biotechnology Value Fund II, L.P. Delaware BVF II GP LLC Delaware Biotechnology Value Trading Fund OS LP Cayman Islands BVF Partners OS Ltd. Cayman Islands BVF GP Holdings LLC Delaware BVF Partners L.P. Delaware BVF Inc. Delaware Mark N. Lampert United States

Filing person

Biotechnology Value Fund, L.P. ("BVF") BVF I GP LLC ("BVF GP") Biotechnology Value Fund II, L.P. ("BVF2") BVF II GP LLC ("BVF2 GP") Biotechnology Value Trading Fund OS LP ("Trading Fund OS") BVF Partners OS Ltd. ("Partners OS") BVF GP Holdings LLC ("BVF GPH") BVF Partners L.P. ("Partners") BVF Inc. Mark N. Lampert ("Mr. Lampert") Each of the foregoing is referred to as a "Reporting Person" and collectively as the "Reporting Persons."

Principal business or residence address

Biotechnology Value Fund, L.P. 44 Montgomery St., 40th Floor San Francisco, California 94104 BVF I GP LLC 44 Montgomery St., 40th Floor San Francisco, California 94104 Biotechnology Value Fund II, L.P. 44 Montgomery St., 40th Floor San Francisco, California 94104 BVF II GP LLC 44 Montgomery St., 40th Floor San Francisco, California 94104 Biotechnology Value Trading Fund OS LP PO Box 309 Ugland House Grand Cayman, KY1-1104 Cayman Islands BVF Partners OS Ltd. PO Box 309 Ugland House Grand Cayman, KY1-1104 Cayman Islands BVF GP Holdings LLC 44 Montgomery St., 40th Floor San Francisco, California 94104 BVF Partners L.P. 44 Montgomery St., 40th Floor San Francisco, California 94104 BVF Inc. 44 Montgomery St., 40th Floor San Francisco, California 94104 Mark N. Lampert 44 Montgomery St., 40th Floor San Francisco, California 94104

Not applicable indication

Y

Percent of class

The following percentages are based on 64,526,242 Shares outstanding as of July 30, 2026, which is the total number of Shares outstanding as reported in the Issuer's Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission on August 3, 2026. As of the close of business on September 30, 2026, (i) BVF beneficially owned approximately 2.9% of the outstanding Shares, (ii) BVF2 beneficially owned approximately 2.2% of the outstanding Shares, (iii) Trading Fund OS beneficially owned less than 1% of the outstanding Shares, (iv) BVF GP may be deemed to beneficially own approximately 2.9% of the outstanding Shares, (v) BVF2 GP may be deemed to beneficially own approximately 2.2% of the outstanding Shares, (vi) Partners OS may be deemed to beneficially own less than 1% of the outstanding Shares, (vii) BVF GPH may be deemed to beneficially own approximately 5.1% of the outstanding Shares, and (viii) each of Partners, BVF Inc. and Mr. Lampert may be deemed to beneficially own approximately 5.6% of the outstanding Shares (less than 1% of the outstanding Shares are held in the Partners Managed Account).

Amount beneficially owned

As of the close of business on September 30, 2026, (i) BVF beneficially owned 1,866,761 shares of the Issuer's Common Stock, $0.0001 par value per share (the "Shares"), (ii) BVF2 beneficially owned 1,404,263 Shares and (iii) Trading Fund OS beneficially owned 261,006 Shares. BVF GP, as the general partner of BVF, may be deemed to beneficially own the 1,866,761 Shares beneficially owned by BVF. BVF2 GP, as the general partner of BVF2, may be deemed to beneficially own the 1,404,263 Shares beneficially owned by BVF2. Partners OS, as the general partner of Trading Fund OS, may be deemed to beneficially own the 261,006 Shares beneficially owned by Trading Fund OS. BVF GPH, as the sole member of each of BVF GP and BVF2 GP, may be deemed to beneficially own the 3,271,024 Shares beneficially owned in the aggregate by BVF and BVF2. Partners, as the investment manager of BVF, BVF2 and Trading Fund OS, and the sole member of Partners OS, may be deemed to beneficially own the 3,608,968 Shares beneficially owned in the aggregate by BVF, BVF2 and Trading Fund OS and held in a certain Partners managed account (the "Partners Managed Account"), including 76,938 Shares held in the Partners Managed Account. BVF Inc., as the general partner of Partners, may be deemed to beneficially own the 3,608,968 Shares beneficially owned by Partners. Mr. Lampert, as a director and officer of BVF Inc., may be deemed to beneficially own the 3,608,968 Shares beneficially owned by BVF Inc. The foregoing should not be construed in and of itself as an admission by any Reporting Person as to beneficial ownership of any Shares owned by another Reporting Person. BVF GP disclaims beneficial ownership of the Shares beneficially owned by BVF. BVF2 GP disclaims beneficial ownership of the Shares beneficially owned by BVF2. Partners OS disclaims beneficial ownership of the Shares beneficially owned by Trading Fund OS. BVF GPH disclaims beneficial ownership of the Shares beneficially owned by BVF and BVF2. Each of Partners, BVF Inc. and Mr. Lampert disclaims beneficial ownership of the Shares beneficially owned by BVF, BVF2 and Trading Fund OS and held in the Partners Managed Account, and the filing of this statement shall not be construed as an admission that any such person or entity is the beneficial owner of any such securities.

Sole voting power

See Cover Pages Items 5-9.

Shared voting power

See Cover Pages Items 5-9.

Sole dispositive power

See Cover Pages Items 5-9.

Shared dispositive power

See Cover Pages Items 5-9.

Not applicable indication

Y

Not applicable indication

N

Ownership on behalf of another person

BVF GPH, Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by BVF and BVF2. Partners, BVF Inc. and Mr. Lampert share voting and dispositive power over the Shares beneficially owned by Trading Fund OS and held in the Partners Managed Account.

Not applicable indication

Y

Not applicable indication

N

Group members

See Exhibit 99.1.

Not applicable indication

Y

Not applicable indication

N

Certifications

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.

99.1 - Joint Filing Agreement, September 30, 2026.