ClinVar Miner

Submissions for variant NM_001278116.2(L1CAM):c.2302G>A (p.Val768Ile)

gnomAD frequency: 0.00178  dbSNP: rs36021462
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000439917 SCV000110592 uncertain significance not provided 2014-09-08 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000194324 SCV000247785 likely benign not specified 2015-11-24 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000194324 SCV000304108 likely benign not specified criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000439917 SCV000511247 benign not provided 2016-09-14 criteria provided, single submitter clinical testing
Invitae RCV001083170 SCV000629391 benign Spastic paraplegia 2021-12-16 criteria provided, single submitter clinical testing
Ambry Genetics RCV000717826 SCV000848686 benign History of neurodevelopmental disorder 2017-01-09 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV000439917 SCV001758011 benign not provided 2015-03-03 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 30487145, 22222883, 9268105)
Athena Diagnostics Inc RCV000194324 SCV001879555 benign not specified 2020-11-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000194324 SCV002103477 benign not specified 2022-02-23 criteria provided, single submitter clinical testing Variant summary: L1CAM c.2302G>A (p.Val768Ile) results in a 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 0.0021 in 204982 control chromosomes, predominantly at a frequency of 0.0063 within the South Asian subpopulation in the gnomAD database. This frequency is not significantly higher than expected for a pathogenic variant in L1CAM causing L1 Syndrome (0.0021 vs 0.0065), allowing no conclusion about variant significance. Although reported in the literature, to our knowledge, no occurrence/penetrant association of c.2302G>A in individuals affected with L1 Syndrome and no supporting experimental evidence demonstrating its impact on protein function have been reported. Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Genome Diagnostics Laboratory,The Hospital for Sick Children RCV001847649 SCV002105404 likely benign Hereditary spastic paraplegia 2017-07-18 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000439917 SCV001743567 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000439917 SCV001800356 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000439917 SCV001966258 likely benign not provided no assertion criteria provided clinical testing

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