ClinVar Miner

Submissions for variant NM_138927.4(SON):c.245-485_273delinsGTTG

dbSNP: rs2085688464
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV001291654 SCV001480230 likely pathogenic ZTTK syndrome 2020-07-09 criteria provided, single submitter clinical testing The c.245-485_273delinsGTTG variant identified in this individual is a de novo deletion (514bp) and insertion (4bp) variant spanning the intron 2 and part of the coding exon 3 (NM_138927.3), predicted to result in the splice junction loss and deletionof 10 codons (amino acid residues 82-91). Exon 3 is the largest coding exon in the SON transcript encoding1972 out of 2426 total amino acids (81%of the protein). The deleted region is present in all the SON Refseq coding transcripts. The variant is absent from gnomAD, suggesting it is not a common benign variant in the populations represented in these databases. This variant is not identified in ClinVar, and to our current knowledge has not been identified in any affected individuals in the literature. Given the predicted deleterious nature of this deletion insertion variant (splice junction loss) and its absence in population databases, the c.245-485_273delinsGTTG identified in the SON gene is reported here as Likely Pathogenic.

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