ClinVar Miner

Submissions for variant NM_024577.3(SH3TC2):c.1862G>A (p.Arg621His) (rs143032801)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000724178 SCV000225418 uncertain significance not provided 2014-12-05 criteria provided, single submitter clinical testing
GeneDx RCV000724178 SCV000292722 uncertain significance not provided 2016-12-29 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SH3TC2 gene. The R621H variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R621H variant is observed in 44/10,252 (0.4%) alleles from individuals of African background (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R621H variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved. However, in silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Athena Diagnostics Inc RCV000236423 SCV000615242 likely benign not specified 2017-03-29 criteria provided, single submitter clinical testing
Invitae RCV001085590 SCV000776116 likely benign Charcot-Marie-Tooth disease type 4 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001157383 SCV001318951 likely benign Mononeuropathy of the median nerve, mild 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Clinical Services Laboratory,Illumina RCV001157384 SCV001318952 likely benign Charcot-Marie-Tooth disease, type 4C 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Molecular Genetics Laboratory,London Health Sciences Centre RCV001173837 SCV001336953 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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