ClinVar Miner

Submissions for variant NM_005765.3(ATP6AP2):c.922A>C (p.Asn308His)

gnomAD frequency: 0.00009  dbSNP: rs756836341
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001712212 SCV000518333 likely benign not provided 2018-04-05 criteria provided, single submitter clinical testing
Invitae RCV000538751 SCV000640013 uncertain significance Syndromic X-linked intellectual disability Hedera type 2024-02-01 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with histidine, which is basic and polar, at codon 308 of the ATP6AP2 protein (p.Asn308His). This variant is present in population databases (rs756836341, gnomAD 0.05%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with ATP6AP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 380358). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ATP6AP2 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Ambry Genetics RCV002524871 SCV003649806 likely benign Inborn genetic diseases 2022-06-03 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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