enGene Holdings Inc.

Evaluation of Disclosure Controls and Procedures

As of the end of the period covered by this Quarterly Report, management, under the supervision of and with the participation of our Chief Executive Officer (principal executive officer) and Chief Financial Officer (principal financial officer and principal accounting officer), carried out an evaluation of the effectiveness of the design and operation of our disclosure controls and procedures (as defined in Rules 13a-15(e) and 15d-15(e) under the Securities Exchange Act of 1934, as amended (the “Exchange Act”)).

As discussed in our Annual Report on Form 10-K for the year ended October 31, 2024, the Company previously concluded that material weaknesses, as defined under the Exchange Act, existed in our internal control over financial reporting for each of the fiscal years ended 2024, 2023 and 2022. Although certain of these material weaknesses were remediated as of October 31, 2024, three of these material weaknesses remain outstanding as of July 31, 2025.

Based on our assessment, our management, including our principal executive officer and our principal financial officer, concluded that, as of July 31, 2025, our disclosure controls and procedures were not effective due to the remaining unremediated material weaknesses in internal controls over financial reporting, as further described below.

Material Weakness in Internal Control Over Financial Reporting

A material weakness is a deficiency, or a combination of deficiencies, in internal control over financial reporting such that there is a reasonable possibility that a material misstatement of our consolidated financial statements will not be prevented or detected on a timely basis. The following three material weaknesses in internal control over financial reporting remain unremediated as of July 31, 2025:

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lack of formal policies, procedures and controls related to the design of internal controls over financial reporting, including risk assessment process and control activities for certain key financial reporting processes;

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deficiency in design of general information technology controls, primarily related to program change management control and testing, user access control related to segregation of duties and access privileges, systems operations controls related to transfer, storage and recovery of data; and

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lack of appropriate segregation of duties in the preparation and review of account reconciliations and journal entries.

Remediation Efforts

In response to the remaining material weaknesses described above, the Company is undertaking ongoing remediation efforts and implemented the following to address the material weaknesses:

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established adequate review and approval processes and procedures based on roles and responsibilities of each team member;

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implemented a risk assessment over financial reporting controls;

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designed and implemented policy, procedures and controls around key business and financial reporting process;

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enhanced software tools with adequate set up to ensure segregation of duties; and

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engaged a professional accounting services firm to help with the documentation and assessment of our internal controls for complying with the Sarbanes-Oxley Act.

The Company has made significant progress in enhancing its internal controls over financial reporting. As part of our ongoing remediation efforts, we are actively testing the design and operational effectiveness of these controls.

Inherent Limitations on Effectiveness of Controls and Procedures

Our disclosure controls and procedures were developed through a process in which our management applied its judgment in assessing the costs and benefits of such controls and procedures, which, by their nature, can provide only reasonable assurance regarding the control objectives. You should note that the design of any system of disclosure controls and procedures is based in part upon various assumptions about the likelihood of future events, and we cannot assure you that any design will succeed in achieving its stated goals under all potential future conditions, regardless of how remote.

Changes in Internal Control over Financial Reporting

Other than the items discussed above, there were no changes in our internal control over financial reporting (as defined in Rules 13a15(f) and 15d-15(f) under the Exchange Act) that occurred during the quarter ended July 31, 2025 that have materially affected, or are reasonably likely to materially affect, our internal control over financial reporting.