ClinVar Miner

Submissions for variant NM_003680.4(YARS1):c.1099C>T (p.Arg367Trp)

gnomAD frequency: 0.00003  dbSNP: rs376054085
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000687751 SCV000815337 pathogenic Charcot-Marie-Tooth disease dominant intermediate C 2023-09-23 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 567612). For these reasons, this variant has been classified as Pathogenic. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on YARS protein function. This missense change has been observed in individuals with autosomal recessive YARS-related conditions (PMID: 29302074, 31130284, 34536092). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs376054085, gnomAD 0.03%). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 367 of the YARS protein (p.Arg367Trp).
Institute of Human Genetics, University of Leipzig Medical Center RCV001264808 SCV001442999 pathogenic recessive ARS-related multisystem disease 2020-06-01 criteria provided, single submitter clinical testing PS1, PM2, PM3, PP1_Strong, PP3
GeneDx RCV001584557 SCV001812954 likely pathogenic not provided 2024-05-15 criteria provided, single submitter clinical testing 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: 29302074, 31130284, 16429158, 34536092, 38125821)
Athena Diagnostics RCV001662751 SCV001879895 likely benign not specified 2021-05-05 criteria provided, single submitter clinical testing
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV002226737 SCV002505683 pathogenic Neurologic, endocrine, and pancreatic disease, multisystem, infantile-onset 2 2022-05-03 criteria provided, single submitter clinical testing

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