ClinVar Miner

Submissions for variant NM_012309.5(SHANK2):c.2668C>G (p.Pro890Ala)

gnomAD frequency: 0.00001  dbSNP: rs782309898
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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 RCV001291694 SCV001480277 uncertain significance Autism, susceptibility to, 17 2019-10-07 criteria provided, single submitter clinical testing The c.904C>G (p.Pro302Ala) variant identified in the SHANK2 gene substitutes a completely conserved Proline for Alanine at amino acid 302/1262 (coding exon: 10/11). This variant is found with low frequency in gnomAD (4 heterozygotes, 0 homozygotes; allele frequency: 1.51e-5) and ExAC (1 heterozygote, 0 homozygotes; allele frequency: 1.355e-5), suggesting it is not a common benign variant in the populations represented in these databases. In silico algorithms predict this variant to be Deleterious (Provean; score:-6.23) and Damaging (SIFT; score: 0.017) to the function of the canonical transcript. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. Given the lack of compelling evidence for its pathogenicity, the c.904C>G (p.Pro302Ala) variant identified in SHANK2 is reported here as a Variant of Uncertain Significance.

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