Syndax Pharmaceuticals Inc Income Taxes Disclosure

17. Income Taxes

For the years ending December 31, 2025, and December 31, 2024, the Company recognized current state income tax expense of $0.4 million and $0.3 million, respectively, recorded under selling, general and administrative expense. The Company’s current year profit and historical losses before income tax for the periods presented was generated entirely in the United States.

As previously disclosed for the years ended December 31, 2024, and 2023, prior to the adoption of ASU 2023-09, the following is a reconciliation of the difference between the effective income tax rate and the federal statutory rate:

The One Big Beautiful Bill Act, or OBBBA, was signed into law on July 4, 2025. The OBBBA includes significant changes affecting business taxpayers, with various effective dates. Among the provisions impacting the Company is Section 174A, which permits current expensing of domestic research and experimental, or R&E, expenditures. The Company elected to currently deduct domestic R&E costs incurred during the year and did not elect to accelerate deductions for domestic R&E costs capitalized in prior years. Foreign R&E expenditures continue to be amortized over 15 years under Section 174.

For the fiscal year ended December 31, 2025, the Company was subject to the Section 163(j) business interest expense limitation based on its average annual gross receipts (as determined under Section 448(c)). For tax

years beginning after December 31, 2024, the OBBBA modifies the Section 163(j) Adjusted Taxable Income (“ATI”) calculation to allow an add-back for depreciation and amortization.

The Company has provided a valuation allowance for the full amount of the net deferred tax assets as the realization of the deferred tax assets is not determined to be more likely than not. The valuation allowance increased by $81.1 million in 2025 due to the increase in deferred tax assets, primarily driven by the generation of net operating losses, and capitalized research expenses. The valuation allowance increased by $52.7 million in 2024 due to the increase in deferred tax assets, primarily driven by the generation of net operating losses and capitalized research expenses, and capitalized start-up costs.

As of December 31, 2025, the Company had approximately $585.3 million and $227.7 million in federal and state net operating losses, or NOLs, respectively, which may be available to offset future taxable income. The Company has generated federal NOLs of $563.2 million and state NOLs of $8.7 million which have indefinite carryforward period. The remaining $22.1 million of federal NOLs and $219.0 million the Company’s state NOLs will begin to expire at various dates starting in 2026. Effective January 1, 2024, the Company has been reclassified as an active trade or business for tax purposes. This resulted in a reclassification of capitalized start-up and other costs to net operating losses and valuation allowance in the 2025 tax statements.

As of December 31, 2025, the Company had available research and development and orphan drug tax credits of approximately $9.8 million and $27.0 million, respectively. Income tax credits began to expire in 2024.

Realization of future tax benefits is dependent on many factors, including the Company’s ability to generate taxable income within the net operating loss carryforward period. Under the Internal Revenue Code provisions, certain substantial changes in the Company’s ownership, including the sale of the Company or significant changes in ownership due to sales of equity, may have limited, or may limit in the future, the amount of net operating loss carryforwards which could be used annually to offset future taxable income. The Company last completed an analysis from January 1, 2023 through December 31, 2023 and determined that no ownership changes had occurred in that period. Prior analyses determined that on March 30, 2007, August 21, 2015 and May 4, 2020, ownership changes had occurred. The Company may also experience ownership changes in the future as a result of subsequent shifts in our stock ownership, some of which may be outside of our control. As a result, its ability to use its pre- change NOLs to offset U.S. federal taxable income may be subject to limitations, which could potentially result in increased future tax liability. In addition, at the state level, there may be periods during which the use of NOLs is suspended or otherwise limited, which could accelerate or permanently increase state taxes owed.

As of December 31, 2025, and 2024, the Company had uncertain tax positions of $0.1 million related to research and development credits, which reduce the deferred tax assets with a corresponding decrease to the valuation allowance. The Company has elected to recognize interest and penalties related to income tax matters as a component of income tax expense, of which no interest or penalties were recorded for the years ended December 31, 2025 and 2024. The Company expects none of the unrecognized tax benefits to decrease within the next 12 months related to expired statutes or settlement with the taxing authorities. Due to the Company’s valuation allowance as of December 31, 2025, none of the Company’s unrecognized tax benefits, if recognized, would affect the effective tax rate.

The Company files tax returns in the U.S. and various states. All tax years since inception (October 11, 2005) remain open to examination by major tax jurisdictions to which the Company is subject, as carryforward attributes generated in years past may still be adjusted upon examination by the Internal Revenue Service or state tax authorities if they have or will be used in a future period. The Company is currently not under examination by the Internal Revenue Service or any other jurisdictions for any tax years.