My initial trouble initially missing - it's relative (6)
I believe the answer is:
mother
'it's relative' is the definition.
(mother is a kind of relative)
'my initial trouble initially missing' is the wordplay.
'initial' says to take the initial letters.
'trouble' becomes 'bother' (synonyms).
'initially missing' means to remove the first letter.
The initial letter of 'my' is 'm'.
'bother' with its first letter taken away is 'other'.
'm'+'other'='MOTHER'
(Other definitions for mother that I've seen before include "Parent to her Tom, oddly" , "- - 7 across, pantomime" , "Nature so-called" , "One who pours the tea?" , "She gave birth to her Tom" .)