ClinVar Miner

Submissions for variant NM_016156.5(MTMR2):c.1855T>C (p.Ser619Pro) (rs116750638)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001084287 SCV000290180 benign Charcot-Marie-Tooth disease type 4 2019-12-31 criteria provided, single submitter clinical testing
Athena Diagnostics Inc RCV000219297 SCV000614130 benign not provided 2019-04-10 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001112850 SCV001270554 uncertain significance Charcot-Marie-Tooth disease, type 4B1 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Molecular Genetics Laboratory,London Health Sciences Centre RCV001172718 SCV001335784 likely benign Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001112850 SCV001472296 benign Charcot-Marie-Tooth disease, type 4B1 2020-02-23 criteria provided, single submitter clinical testing
GeneDx RCV000219297 SCV000279113 not provided not provided 2016-07-15 no assertion provided clinical testing The S619P variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The NHLBI Exome Sequencing Project reports S619P was observed in 21/8596 (0.2%) alleles from individuals of European background. The 1000 Genomes Project reports S619P was observed in 17/978 (1.7%) alleles from individuals of South Asian background and in 6/206 (3.0%) alleles from individuals of Gujarati Indian background, indicating it may be a rare (benign) variant in these populations. The S619P variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is 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.

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