ClinVar Miner

Submissions for variant NM_138361.5(LRSAM1):c.586G>A (p.Gly196Ser) (rs148059394)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000237057 SCV000292609 uncertain significance not provided 2017-12-15 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the LRSAM1 gene. The G196S variant hasnot been published as a pathogenic variant, nor has it been reported as a benign variant to ourknowledge. The G196S variant is observed in 40/33320 (0.1%) alleles from individuals of Latinobackground in large population cohorts (Lek et al., 2016). The G196S variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ inpolarity, charge, size and/or other properties. In-silico analyses, including protein predictors andevolutionary conservation, support a deleterious effect. However, this variant is not predicted to affect the RING domain. Therefore, based on the currently available information, it is unclear whetherthis variant is a pathogenic variant or a rare benign variant.
Invitae RCV001086245 SCV000547856 likely benign Charcot-Marie-Tooth disease type 2P 2019-12-31 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000237057 SCV001155725 uncertain significance not provided 2016-06-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001086245 SCV001331878 likely benign Charcot-Marie-Tooth disease type 2P 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 RCV001173643 SCV001336745 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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