ClinVar Miner

Submissions for variant NM_014225.6(PPP2R1A):c.539T>C (p.Met180Thr)

dbSNP: rs1600167941
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Molecular Medicine, Children’s Hospital of Fudan University RCV003232134 SCV003930300 pathogenic Microcephaly-corpus callosum hypoplasia-intellectual disability-facial dysmorphism syndrome 2023-01-18 criteria provided, single submitter clinical testing
Invitae RCV003558607 SCV004298440 pathogenic not provided 2023-03-26 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change replaces methionine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 180 of the PPP2R1A protein (p.Met180Thr). This missense change has been observed in individual(s) with clinical features of PPP2R1A-related conditions (PMID: 31785789, 33106617). In at least one individual the variant was observed to be de novo. For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Met180 amino acid residue in PPP2R1A. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 33106617; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects PPP2R1A function (PMID: 33106617). 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 PPP2R1A protein function. ClinVar contains an entry for this variant (Variation ID: 684494).
GenomeConnect, ClinGen RCV000844990 SCV000986817 not provided PPP2R1A-related disorder no assertion provided phenotyping only Variant interpretted as pathogenic and reported on 05/04/2018 by GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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