ClinVar Miner

Submissions for variant NM_201384.3(PLEC):c.4556C>T (p.Ser1519Leu)

gnomAD frequency: 0.00112  dbSNP: rs182120395
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000078868 SCV000110728 benign not specified 2015-08-18 criteria provided, single submitter clinical testing
GeneDx RCV000544997 SCV000514139 likely benign not provided 2019-12-10 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001086335 SCV000650285 benign Epidermolysis bullosa simplex 5B, with muscular dystrophy; Epidermolysis bullosa simplex, Ogna type; Epidermolysis bullosa simplex 5C, with pyloric atresia; Autosomal recessive limb-girdle muscular dystrophy type 2Q; Epidermolysis bullosa simplex with nail dystrophy 2024-01-15 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000544997 SCV001145081 benign not provided 2019-07-24 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000544997 SCV001155537 uncertain significance not provided 2019-04-01 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000078868 SCV004804117 likely benign not specified 2024-01-04 criteria provided, single submitter clinical testing Variant summary: PLEC1 c.4637C>T (p.Ser1546Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.0013 in 1566678 control chromosomes, predominantly at a frequency of 0.0015 within the Non-Finnish European subpopulation, including 1 homozygotes, and a frequency of 0.0037 in the Finnish European population in the gnomAD database (v 4.0.0). To our knowledge, no occurrence of c.4637C>T in individuals affected with PLEC1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. Five submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as benign/likely benign (n=4) and VUS (n=1). Based on the evidence outlined above, the variant was classified as likely benign.
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000544997 SCV002036559 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000544997 SCV002038079 likely benign not provided no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV004737185 SCV005347344 likely benign PLEC-related disorder 2024-08-19 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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