The clock for the FREQM bus interface (CLK_APB_FREQM) is enabled and disabled by the Main Clock Controller, the default state of CLK_APB_FREQM can be found in Peripheral Clock Masking.
Two generic clocks are used by the FREQM: Reference Clock (GCLK_FREQM_REF) and Measurement Clock (GCLK_FREQM_MSR).
GCLK_FREQM_REF is required to clock the internal reference timer, which acts as the frequency reference.
GCLK_FREQM_MSR is required to clock a ripple counter for frequency measurement. These clocks must be configured and enabled in the generic clock controller before using the FREQM.