DNLI · Denali Therapeutics Inc.

Reflects an in-kind charitable contribution of 32,220 shares of DNLI to a donor advised fund.

The shares are held of record by the Watts Family 2015 Trust dated July 7, 2015, for which the Reporting Person serves as trustee.

Shares sold to satisfy the tax obligations by the Reporting Person in connection with the settlement of previously vested RSUs.

Includes 135,475 Unvested RSUs.

Includes 1,792 shares acquired under the ESPP Purchase on June 1, 2026.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 restricted stock units (each, an "RSU") payable solely in common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") granted by the Issuer to Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC (the "Adviser GP") on June 3, 2026, pursuant to the Issuer's 2017 Equity Incentive Plan and Outside Director Compensation Policy (collectively the "Incentive Plan"). The RSUs vest on the earlier of June 3, 2027 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2026, subject to Julian C. Baker's continuous service on the board of directors of the Issuer (the "Board") through such vesting date. Julian C. Baker serves on the Board as a representative of 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences", and together with 667, the "Funds") and their affiliates and control persons.

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds or for the benefit of the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

Pursuant to the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 6,408 RSUs on Table I and 19,226 Stock Options on Table II. These grants, totaling 6,408 RSUs and 19,226 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

Includes beneficial ownership of 2,641 shares of Common Stock received previously from vested RSUs and 7,924 shares of Common Stock underlying unvested RSUs that were issued to Julian C. Baker in his capacity as a director of the Issuer, each of which the Funds are deemed to own a portion.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in Common Stock reported in column 5 of Table I and the Stock Options reported in column 9 of Table II held directly by or held for the benefit of Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

19,226 Stock Options exercisable solely into Common Stock were granted under the Incentive Plan to Julian C. Baker in his capacity as a director of the Issuer. The Stock Options have a strike price of $19.66 and expire on June 3, 2036. The Stock Options vest on the earlier of June 3, 2027 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2026, subject to Julian C. Baker's continuous service on the Board through such vesting date.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in Common Stock reported in column 5 of Table I and the Stock Options (as defined below) reported in column 9 of Table II held directly by or held for the benefit of 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667.

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds or for the benefit of the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

Pursuant to the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 6,408 RSUs on Table I and 19,226 Stock Options on Table II. These grants, totaling 6,408 RSUs and 19,226 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

Includes 6,408 restricted stock units (each, an "RSU") payable solely in common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") granted by the Issuer to Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC (the "Adviser GP") on June 3, 2026, pursuant to the Issuer's 2017 Equity Incentive Plan and Outside Director Compensation Policy (collectively the "Incentive Plan"). The RSUs vest on the earlier of June 3, 2027 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2026, subject to Julian C. Baker's continuous service on the board of directors of the Issuer (the "Board") through such vesting date. Julian C. Baker serves on the Board as a representative of 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences", and together with 667, the "Funds") and their affiliates and control persons.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in Common Stock reported in column 5 of Table I and the Stock Options (as defined below) reported in column 9 of Table II held directly by or held for the benefit of 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667.

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds or for the benefit of the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

Pursuant to the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 6,408 RSUs on Table I and 19,226 Stock Options on Table II. These grants, totaling 6,408 RSUs and 19,226 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

Includes beneficial ownership of 2,641 shares of Common Stock received previously from vested RSUs and 7,924 shares of Common Stock underlying unvested RSUs that were issued to Julian C. Baker in his capacity as a director of the Issuer, each of which the Funds are deemed to own a portion.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 17,040 unvested RSUs.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

19,226 Stock Options exercisable solely into Common Stock were granted under the Incentive Plan to Julian C. Baker in his capacity as a director of the Issuer. The Stock Options have a strike price of $19.66 and expire on June 3, 2036. The Stock Options vest on the earlier of June 3, 2027 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2026, subject to Julian C. Baker's continuous service on the Board through such vesting date.

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds or for the benefit of the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

Pursuant to the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 6,408 RSUs on Table I and 19,226 Stock Options on Table II. These grants, totaling 6,408 RSUs and 19,226 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in Common Stock reported in column 5 of Table I and the Stock Options reported in column 9 of Table II held directly by or held for the benefit of Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,408 unvested RSUs.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Shares sold to satisfy the tax obligations by the Reporting Person in connection with the settlement of previously vested RSUs.

Includes 184,915 Unvested RSUs.

Shares sold to satisfy the tax obligations by the Reporting Person in connection with the settlement of previously vested RSUs.

Includes 141,100 Unvested RSUs.

25% of the shares subject to the option shall vest on January 3, 2027, and 1/48 of the shares subject to the option shall vest each month thereafter, subject to the Reporting Person remaining a service provider of the Issuer through each such date.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 25% of the RSUs shall vest on January 3, 2027 (the "Vesting Commencement Date") and an additional 25% of the RSUs shall vest on each annual anniversary of the Vesting Commencement Date thereafter, subject to the Reporting Person remaining a service provider of the Issuer through each such date.

Includes 141,100 Unvested RSUs.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 25% of the RSUs shall vest on January 3, 2027 (the "Vesting Commencement Date") and an additional 25% of the RSUs shall vest on each annual anniversary of the Vesting Commencement Date thereafter, subject to the Reporting Person remaining a service provider of the Issuer through each such date.

Includes 184,915 Unvested RSUs.

25% of the shares subject to the option shall vest on January 3, 2027, and 1/48 of the shares subject to the option shall vest each month thereafter, subject to the Reporting Person remaining a service provider of the Issuer through each such date

667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences" and together with 667, the "Funds") purchased, respectively, 190,523 and 2,095,191 warrants to purchase common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") at an exercise price of $0.01 per share with no expiration date ("$0.01 Prefunded Warrants") for $17.49 per share in a public offering that closed on December 11, 2025.

The $0.01 Prefunded Warrants are exercisable at any time, at the holder's election, on a 1-for-1 basis into Common Stock to the extent that immediately prior to or after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more thn 4.99% of the outstanding shares of Common Stock (the "Maximum Percentage"). By written notice to the Issuer, the Funds may increase or decrease the Maximum Percentage applicable to that fund to any other percentage not in excess of 19.99%; provided that any such increase will not be effective until the 61st day after such notice is delivered to the Issuer.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Biotech Capital, L.P. and (ii) 667, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly by 667, a limited partnership of which the sole general partner is Baker Biotech Capital, L.P., a limited partnership of which the sole general partner is Baker Biotech Capital (GP), LLC, due to their interest in 667 and Baker Biotech Capital, L.P.'s right to receive an allocation of a portion of the profits from 667.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences" and together with 667, the "Funds") purchased, respectively, 190,523 and 2,095,191 warrants to purchase common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") at an exercise price of $0.01 per share with no expiration date ("$0.01 Prefunded Warrants") for $17.49 per share in a public offering that closed on December 11, 2025.

The $0.01 Prefunded Warrants are exercisable at any time, at the holder's election, on a 1-for-1 basis into Common Stock to the extent that immediately prior to or after giving effect to such exercise the holders thereof, together with their affiliates and any members of a Section 13(d) group with such holders, would beneficially own, for purposes of Rule 13d-3 under the Securities Act of 1934, as amended, no more thn 4.99% of the outstanding shares of Common Stock (the "Maximum Percentage"). By written notice to the Issuer, the Funds may increase or decrease the Maximum Percentage applicable to that fund to any other percentage not in excess of 19.99%; provided that any such increase will not be effective until the 61st day after such notice is delivered to the Issuer.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in the securities reported in column 9 of Table II held directly by Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

25% of the shares subject to the option shall vest on November 4, 2026, and an additional 1/48 of the shares subject to the option vest each month thereafter, subject to the Reporting Person remaining a non-employee director of the Issuer through each such date

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. The RSU award vests over a four-year period, with 1/4th of the shares vesting on each anniversary of the grant date (or, for the last tranche that otherwise would vest on the fourth anniversary of the grant date, on such anniversary or, if earlier, on the day prior to the Company's next annual meeting of stockholders occurring after the third anniversary of the grant date), provided that he remains a non-employee director through the applicable vesting date.

Includes 10,632 unvested RSUs.

Reflects an in-kind charitable contribution of 50,000 shares of DNLI to a donor advised fund.

The shares are held of record by the Watts Family 2015 Trust dated July 7, 2015, for which the Reporting Person serves as trustee.

The sales reported by the Reporting Person were affected pursuant to a Rule 10b5-1 trading plan adopted December 11, 2024.

Includes 128,405 Unvested RSUs.

Shares sold to satisfy the tax obligations by the Reporting Person in connection with the settlement of previously vested restricted stock units.

The sale price reported in column 4 of Table I represents the weighted average sale price of the shares ranging from $13.35 to $13.58 per share. Upon request by the Commission staff, the Issuer, or a security holder of the Issuer, the Reporting Person will provide full information regarding the number of shares sold at each separate price.

Includes 128,405 Unvested RSUs.

Includes 975 shares acquired under the ESPP Purchase on June 2, 2025.

Shares sold to satisfy the tax obligations by the Reporting Person in connection with the settlement of previously vested restricted stock units.

The sale price reported in column 4 of Table I represents the weighted average sale price of the shares ranging from $13.34 to $13.58 per share. Upon request by the Commission staff, the Issuer, or a security holder of the Issuer, the Reporting Person will provide full information regarding the number of shares sold at each separate price.

Includes 128,405 Unvested RSUs.

Includes 134,030 Unvested RSUs.

The vesting of the shares subject to the option are contingent upon the achievement of certain performance metrics. 50% of the shares subject to the option vested on March 3, 2021, and 50% of the shares subject to the option will vest on the date the closing price of Issuer's Common Stock equals or exceeds $80.00 per share on NASDAQ for 90 consecutive trading days.

Includes 177,940 Unvested RSUs.

Includes 177,940 Unvested RSUs.

The vesting of the shares subject to the option are contingent upon the achievement of certain performance metrics. 50% of the shares subject to the option vested on March 3, 2021, and 50% of the shares subject to the option will vest on the date the closing price of Issuer's Common Stock equals or exceeds $80.00 per share on NASDAQ for 90 consecutive trading days.

25% of the shares subject to the option will vest on March 8, 2018 and an additional 1/48 of the shares vest monthly thereafter.

The sales reported by the Reporting Person were made pursuant to a previously signed/adopted 10b5-1 Selling plan dated 09/16/2024. The shares sold primarily relate to 455,282 stock options that expire on 08/21/2025.

The sale price reported in column 4 of Table I represents the weighted average sale price of the shares ranging from $15.00 to $15.08 per share. Upon request by the Commission staff, the Issuer, or a security holder of the Issuer, the Reporting Person will provide full information regarding the number of shares sold at each separate price.

Includes 177,940 Unvested RSUs.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,037 unvested RSUs.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 10,565 restricted stock units (each, an "RSU") payable solely in common stock ("Common Stock") of Denali Therapeutics Inc. (the "Issuer") granted by the Issuer to Julian C. Baker, a managing member of Baker Bros. Advisors (GP) LLC (the "Adviser GP") on June 3, 2025, pursuant to the Issuer's 2017 Equity Incentive Plan and Outside Director Compensation Policy (collectively "Incentive Plan"). The RSUs vest in four equal annual installments on June 3, 2026, June 3, 2027, June 3, 2028, and the earlier of June 3, 2029 or the day prior to the Issuer's Annual Meeting occurring after June 3, 2028, in each case subject to Julian C. Baker's continuous service on the board of directors of the Issuer (the "Board") through such vesting dates. Julian C. Baker serves on the Board as a representative of 667, L.P. ("667") and Baker Brothers Life Sciences, L.P. ("Life Sciences", and together with 667, the "Funds") and their affiliates and control persons.

Pursuant to the policies of the Adviser, Julian C. Baker does not have a right to any of the Issuer's securities issued as compensation for his service on the Board and the Funds are entitled to an indirect proportionate pecuniary interest in such securities. The Funds each own an indirect proportionate pecuniary interest in the non-qualified stock options exercisable solely into Common Stock ("Stock Options") and RSUs. Solely as a result of their ownership interest in (i) the general partners of the Funds and (ii) the Funds, Felix J. Baker and Julian C. Baker may be deemed to have an indirect pecuniary interest in the Stock Options, RSUs and any Common Stock acquired upon the exercise of Stock Options or vesting of RSUs (i.e. no direct pecuniary interest) issued as compensation for such Board Service.

Baker Bros. Advisors LP (the "Adviser") serves as the investment adviser to the Funds. In connection with the services provided by the Adviser, the Adviser receives an asset-based management fee that does not confer any pecuniary interest in the securities held directly by the Funds or for the benefit of the Funds. The Adviser GP is the Adviser's sole general partner. Julian C. Baker and Felix J. Baker are managing members of the Adviser GP. The Adviser has complete and unlimited discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds. The general partners of the Funds relinquished to the Adviser all discretion and authority with respect to the investment and voting power of the securities held directly by the Funds or for the benefit of the Funds.

Julian C. Baker, Felix J. Baker, the Adviser GP and the Adviser disclaim beneficial ownership of the securities held directly by or held for the benefit of the Funds except to the extent of their pecuniary interest therein, and this report shall not be deemed an admission that any of Julian C. Baker, Felix J. Baker, the Adviser GP or the Adviser is a beneficial owner of such securities for purposes of Section 16 or any other purpose.

Pursuant the policies of the Adviser, the Adviser has voting and dispositive power over the Stock Options, RSUs and any Common Stock received as a result of the exercise of Stock Options or vesting of RSUs.

The acquisitions of the RSUs and Stock Options reported on this form represent a single grant to Julian C. Baker of 10,565 RSUs on Table I and 31,695 Stock Options on Table II. These grants, totaling 10,565 RSUs and 31,695 Stock Options for Julian C. Baker, are reported for each of the Funds as each has an indirect pecuniary interest in such securities.

After giving effect to the transactions reported herein and as a result of their ownership interest in (i) Baker Brothers Life Sciences Capital, L.P. and (ii) Life Sciences, Julian C. Baker and Felix J. Baker each may be deemed to have an indirect pecuniary interest in Common Stock reported in column 5 of Table I and the Stock Options reported in column 9 of Table II held directly by or held for the benefit of Life Sciences, a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital, L.P., a limited partnership of which the sole general partner is Baker Brothers Life Sciences Capital (GP), LLC, due to their interest in Life Sciences and Baker Brothers Life Sciences Capital, L.P.'s right to receive an allocation of a portion of the profits from Life Sciences.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,037 unvested RSUs.

100% of the shares subject to the option shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,037 unvested RSUs.

Each share is represented by a Restricted Stock Unit ("RSU") and a contingent right to receive one share of common stock of the Issuer. 100% of the RSUs shall vest upon the earlier of (i) the one year anniversary of the grant date or (ii) the day preceding the Issuer's next annual meeting of stockholders occurring after the grant date.

Includes 6,037 unvested RSUs.