ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2869C>T (p.Leu957Phe)

dbSNP: rs142164373
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV000029245 SCV002802463 likely pathogenic Hyperphosphatasia with intellectual disability syndrome 2 2021-11-11 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000029245 SCV003298132 pathogenic Hyperphosphatasia with intellectual disability syndrome 2 2023-06-14 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 PIGO function (PMID: 22683086). 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 not expected to disrupt PIGO protein function. ClinVar contains an entry for this variant (Variation ID: 35599). This missense change has been observed in individual(s) with PIGO-related conditions (PMID: 22683086). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with phenylalanine, which is neutral and non-polar, at codon 957 of the PIGO protein (p.Leu957Phe).
OMIM RCV000029245 SCV000051891 pathogenic Hyperphosphatasia with intellectual disability syndrome 2 2012-07-13 no assertion criteria provided literature only

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