ClinVar Miner

Submissions for variant NM_001312673.2(PCYT1A):c.296C>T (p.Ala99Val)

gnomAD frequency: 0.00003  dbSNP: rs587777189
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine RCV000087314 SCV000266528 pathogenic Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome criteria provided, single submitter research
Ambry Genetics RCV000622339 SCV000741194 pathogenic Inborn genetic diseases 2016-02-04 criteria provided, single submitter clinical testing
Invitae RCV002515781 SCV003525401 pathogenic not provided 2022-02-18 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects PCYT1A function (PMID: 30559292). 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 PCYT1A protein function. ClinVar contains an entry for this variant (Variation ID: 101057). This missense change has been observed in individual(s) with spondylometaphyseal dysplasia with cone-rod dystrophy (PMID: 24387990). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs587777189, gnomAD 0.0009%). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 99 of the PCYT1A protein (p.Ala99Val).
OMIM RCV000087314 SCV000120194 pathogenic Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome 2014-01-02 no assertion criteria provided literature only

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