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how can a DELETION be not a NULL variant?

I've found a var (exam, human) in ROBO2 gene: 3-77684075-ACAG-A According to Varsome this is not a NULL variant. Sorry if it sounds silly, but how can a DELETION not being a NULL variant?

Thanks a lot in advance for any help!

deletion variant exome indel acmg
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by cocchi.e89 cocchi.e89

In the ACMG classification, PVS1 explanation: "Not a null variant."

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written by cocchi.e89 cocchi.e89

1 answer

In genetics, null refers to a complete loss of function. A deletion could be considered not a null if it doesn't abolish completely the function of the gene. For example, deletion of an intronic sequence may have no detectable functional effect or deletion of the C-terminal end of a protein may only partially impair its function.

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written by Jean-Karim Heriche Jean-Karim Heriche

Precisely! In this case it is a deletion of 3 base pairs in the coding region of ROBO2 (ACAG goes to A by loss of CAG). Therefore it is an 'in-frame' deletion, which causes the protein to be shortened by one amino acid residue.

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written by rbagnall rbagnall

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