We are using the LTC6946-3 synthesizer in an application that requires a 5MHz reference oscillator, with the synth reference divider ratio (R counter) set to "1".
The datasheet states a minimum REF input frequency of 10MHz.
Is there any downside to using a 5MHz reference input with this device?
The short answer is 5MHz is ok, but you need to be aware of how this affects performance.
The longer answer is
For the input reference signal the datasheet states a minimum frequency of 10MHz and a minimum slew rate of 20V/us. Using a low ultra low noise reference signal and following these criteria you should be able to meet the datasheets in-band performance specs (1/f noise and FOM) of the LTC6946.
The LTC6946 can perform well with reference frequencies <10MHz, but you will need to ensure the reference slew rate is fast enough to avoid any amplitude noise to phase noise conversion that can occur with slower slew rate signals. The amplitude noise to phase noise conversion on the reference input will affect the in-band performance of the LTC6946.
For a sine wave you can calculate the slew rate (SR) with this equation, SR = 2*pi*Frequency*Vp.
To increase your reference signals slew rate you can use gain and clip techniques, such as the one shown in design note 514. https://www.analog.com/media/en/reference-design-documentation/design-notes/dn514f.pdf
In general faster reference slew rates are better. Also, using a large cap on the reference (1uF) is recommended, but a 4.7uF will give better 1/f performance. Please refer to the datasheet for more information on these capacitors...