Question

To ask Her Majesty's Government what is their estimate of the number of individuals who self-identify as transsexual; and how many individuals have received a Gender Recognition Certificate since the Gender Recognition Act 2004 was passed.

The Government does not have an estimate of the number of individuals in the UK who identify as transgender.
The total transgender population is difficult to estimate for a number of reasons. For example, there is no standardised approach to collecting data on gender identity and some individuals are unwilling to disclose that they are transgender due to privacy concerns.
The Ministry of Justice publish statistics on the Gender Recognition Act process every quarter. The latest statistics can be found at:

https://www.gov.uk/government/statistics/tribunals-and-gender-recognition-certificate-statistics-quarterly-october-to-december-2017