ClinVar Miner

Submissions for variant NM_001312673.2(PCYT1A):c.448C>G (p.Pro150Ala)

dbSNP: rs587777190
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Total submissions: 3
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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 RCV000087315 SCV000266529 pathogenic Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome criteria provided, single submitter research
Invitae RCV001854510 SCV002300816 likely pathogenic not provided 2022-09-13 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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: 101058). This missense change has been observed in individual(s) with spondylometaphyseal dysplasia (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 (rs587777190, gnomAD 0.0009%). This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 150 of the PCYT1A protein (p.Pro150Ala).
OMIM RCV000087315 SCV000120195 pathogenic Spondylometaphyseal dysplasia-cone-rod dystrophy syndrome 2014-01-02 no assertion criteria provided literature only

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