ClinVar Miner

Submissions for variant NM_033419.5(PGAP3):c.851A>G (p.His284Arg)

dbSNP: rs776720232
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Personalized Medicine, Children's Hospital Los Angeles RCV001552976 SCV000854552 pathogenic not provided 2018-11-19 criteria provided, single submitter clinical testing
GeneDx RCV001552976 SCV001773763 pathogenic not provided 2024-12-03 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 28794914, 26077850, 30345601, 30919572, 30755392, 34374989)
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India RCV001194673 SCV002053907 likely pathogenic Hyperphosphatasia with intellectual disability syndrome 4 criteria provided, single submitter research
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV001194673 SCV004807855 pathogenic Hyperphosphatasia with intellectual disability syndrome 4 2024-03-29 criteria provided, single submitter clinical testing
Al Jalila Children’s Genomics Center, Al Jalila Childrens Speciality Hospital RCV001194673 SCV005420517 pathogenic Hyperphosphatasia with intellectual disability syndrome 4 2024-10-04 criteria provided, single submitter research PP1,PM2,PM3(strong),PM5,PM1
Labcorp Genetics (formerly Invitae), Labcorp RCV001552976 SCV005837571 pathogenic not provided 2024-12-02 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 284 of the PGAP3 protein (p.His284Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with hyperphosphatasia with mental retardation syndrome (PMID: 26077850, 28794914, 30345601). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 599004). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt PGAP3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001194673 SCV001364412 pathogenic Hyperphosphatasia with intellectual disability syndrome 4 2022-11-07 no assertion criteria provided literature only

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