ClinVar Miner

Submissions for variant NM_001199107.2(TBC1D24):c.169C>T (p.Arg57Cys) (rs202162520)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189679 SCV000243325 benign not specified 2019-07-22 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000189679 SCV000269860 benign not specified 2015-07-16 criteria provided, single submitter clinical testing p.Arg57Cys in exon 2 of TBC1D24: This variant is not expected to have clinical s ignificance it has been identified in 0.3% (182/65958) of European chromosomes b y the Exome Aggregation Consortium (ExAC,; dbSNP rs202162520).
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000585579 SCV000332349 uncertain significance not provided 2017-02-08 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000340164 SCV000396203 likely benign Myoclonic epilepsy, familial infantile 2018-01-13 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.
Invitae RCV001084629 SCV000560545 benign Epileptic encephalopathy, early infantile, 1; Deafness, autosomal dominant 65; Caused by mutation in the TBC1 domain family, member 24 2020-12-04 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000189679 SCV000615752 uncertain significance not specified 2016-10-17 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000585579 SCV000692828 likely benign not provided 2021-02-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717076 SCV000847922 uncertain significance Seizures 2019-05-01 criteria provided, single submitter clinical testing The p.R57C variant (also known as c.169C>T), located in coding exon 1 of the TBC1D24 gene, results from a C to T substitution at nucleotide position 169. The arginine at codon 57 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on data from gnomAD, the T allele has an overall frequency of approximately 0.18% (507/27762) total alleles studied. The highest observed frequency was 1.06% (107/10138) of Ashkenazi Jewish alleles. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Bioinformatics Core,Luxembourg Center for Systems Biomedicine RCV000656037 SCV000588313 pathogenic Rolandic epilepsy 2017-01-01 no assertion criteria provided case-control CAADphred>15
GenomeConnect, ClinGen RCV000585579 SCV000840178 not provided not provided no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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