ClinVar Miner

Submissions for variant NM_004230.4(S1PR2):c.955G>A (p.Gly319Arg)

gnomAD frequency: 0.00004  dbSNP: rs139097585
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine RCV001195211 SCV001365517 likely benign not specified 2020-02-11 criteria provided, single submitter clinical testing The p.Gly319Arg variant in S1PR2 is classified as likely benign due to a lack of conservation across species. 9 mammals (naked mole rat, guinea pig, chinchilla, brush-tailed rat, Tibetan antelope, cow, sheep, domestic goat and shrew) carry an arginine (ARG) at this position. In addition, computational prediction tools predict that this variant does not impact the protein. It has been identified in 0.014% (2/14686) of African chromosomes by gnomAD (http://gnomad.broadinstitute.org). ACMG/AMP Criteria applied: BP4_Strong.
Labcorp Genetics (formerly Invitae), Labcorp RCV001863082 SCV002268214 uncertain significance not provided 2021-06-24 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with S1PR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 929890). This variant is present in population databases (rs139097585, ExAC 0.01%). This sequence change replaces glycine with arginine at codon 319 of the S1PR2 protein (p.Gly319Arg). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and arginine.
Ambry Genetics RCV004659378 SCV005158931 uncertain significance Inborn genetic diseases 2024-05-28 criteria provided, single submitter clinical testing The c.955G>A (p.G319R) alteration is located in exon 2 (coding exon 1) of the S1PR2 gene. This alteration results from a G to A substitution at nucleotide position 955, causing the glycine (G) at amino acid position 319 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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