Total submissions: 4
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
3billion | RCV000055980 | SCV002521709 | pathogenic | Congenital defect of folate absorption | 2022-05-22 | criteria provided, single submitter | clinical testing | The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.002%). Missense changes are a common disease-causing mechanism. In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.73; 3Cnet: 0.29). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (PMID: 20686069). A different missense change at the same codon (p.Arg376Trp) has been reported to be associated with SLC46A1 related disorder (ClinVar ID: VCV000000854 / PMID: 17446347). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. |
Invitae | RCV000059711 | SCV003273639 | uncertain significance | not provided | 2022-10-24 | criteria provided, single submitter | clinical testing | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 376 of the SLC46A1 protein (p.Arg376Gln). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with autosomal recessive hereditary folate malabsorption (PMID: 21489556). ClinVar contains an entry for this variant (Variation ID: 65749). 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 SLC46A1 protein function. Experimental studies have shown that this missense change affects SLC46A1 function (PMID: 20686069). This variant disrupts the p.Arg376 amino acid residue in SLC46A1. Other variant(s) that disrupt this residue have been observed in individuals with SLC46A1-related conditions (PMID: 17446347), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. |
Gene |
RCV000055980 | SCV000087033 | not provided | Congenital defect of folate absorption | no assertion provided | literature only | ||
Uni |
RCV000059711 | SCV000091281 | not provided | not provided | no assertion provided | not provided |