ClinVar Miner

Submissions for variant NM_000197.2(HSD17B3):c.389A>G (p.Asn130Ser)

gnomAD frequency: 0.00004  dbSNP: rs119481079
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV001818138 SCV002069634 likely pathogenic not provided 2020-09-28 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000005156 SCV004190281 likely pathogenic Testosterone 17-beta-dehydrogenase deficiency 2023-11-20 criteria provided, single submitter clinical testing ACMG:PM1 PM2 PP2 PP3
Invitae RCV001818138 SCV004296026 pathogenic not provided 2024-01-19 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 130 of the HSD17B3 protein (p.Asn130Ser). This variant is present in population databases (rs119481079, gnomAD 0.007%). This missense change has been observed in individual(s) with 17β-HSD3 deficiency (PMID: 25740850, 27307783, 36154887). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 4880). 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) performed at Invitae indicates that this missense variant is expected to disrupt HSD17B3 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects HSD17B3 function (PMID: 9709959). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000005156 SCV000025333 pathogenic Testosterone 17-beta-dehydrogenase deficiency 1998-08-01 no assertion criteria provided literature only

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