Total submissions: 7
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Center for Personalized Medicine, |
RCV001552976 | SCV000854552 | pathogenic | not provided | 2018-11-19 | criteria provided, single submitter | clinical testing | |
Gene |
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, |
RCV001194673 | SCV002053907 | likely pathogenic | Hyperphosphatasia with intellectual disability syndrome 4 | criteria provided, single submitter | research | ||
Genomic Medicine Center of Excellence, |
RCV001194673 | SCV004807855 | pathogenic | Hyperphosphatasia with intellectual disability syndrome 4 | 2024-03-29 | criteria provided, single submitter | clinical testing | |
Al Jalila Children’s Genomics Center, |
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 |
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 |