ClinVar Miner

Submissions for variant NM_024678.6(NARS2):c.506T>A (p.Phe169Tyr)

gnomAD frequency: 0.00001  dbSNP: rs144653284
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics RCV000434134 SCV000511126 uncertain significance not provided 2016-07-11 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
GeneDx RCV000434134 SCV001758412 uncertain significance not provided 2022-01-28 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (gnomAD); 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
Labcorp Genetics (formerly Invitae), Labcorp RCV000434134 SCV002957484 uncertain significance not provided 2022-08-19 criteria provided, single submitter clinical testing This sequence change replaces phenylalanine, which is neutral and non-polar, with tyrosine, which is neutral and polar, at codon 169 of the NARS2 protein (p.Phe169Tyr). This variant is present in population databases (rs144653284, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with NARS2-related conditions. ClinVar contains an entry for this variant (Variation ID: 377031). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The tyrosine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV002521510 SCV003731273 uncertain significance Inborn genetic diseases 2022-08-16 criteria provided, single submitter clinical testing The c.506T>A (p.F169Y) alteration is located in exon 4 (coding exon 4) of the NARS2 gene. This alteration results from a T to A substitution at nucleotide position 506, causing the phenylalanine (F) at amino acid position 169 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
3billion RCV004725210 SCV005328819 likely benign Combined oxidative phosphorylation defect type 24; Hearing loss, autosomal recessive 94 2024-09-20 criteria provided, single submitter clinical testing The homozygous variant was found in patients diagnosed with another variant in a different gene, with no symptoms related to the gene containing the homozygous variant.
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre RCV004820846 SCV005441938 uncertain significance Combined oxidative phosphorylation defect type 24 2024-12-19 criteria provided, single submitter clinical testing

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