ClinVar Miner

Submissions for variant NM_024537.4(CARS2):c.9G>T (p.Arg3Ser)

gnomAD frequency: 0.00011  dbSNP: rs766060435
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001332525 SCV001524881 uncertain significance Combined oxidative phosphorylation defect type 27 2019-05-01 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV001332525 SCV002272666 uncertain significance Combined oxidative phosphorylation defect type 27 2024-11-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 3 of the CARS2 protein (p.Arg3Ser). 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 variant has not been reported in the literature in individuals affected with CARS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1030850). An algorithm developed to predict the effect of missense changes on protein structure and function outputs the following: PolyPhen-2: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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.
Ambry Genetics RCV002546574 SCV003679751 uncertain significance Inborn genetic diseases 2022-03-04 criteria provided, single submitter clinical testing The c.9G>T (p.R3S) alteration is located in exon 1 (coding exon 1) of the CARS2 gene. This alteration results from a G to T substitution at nucleotide position 9, causing the arginine (R) at amino acid position 3 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
GeneDx RCV003169555 SCV003915088 uncertain significance not provided 2023-03-27 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Breakthrough Genomics, Breakthrough Genomics RCV003169555 SCV005192226 uncertain significance not provided criteria provided, single submitter not provided

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