ClinVar Miner

Submissions for variant NM_133642.5(LARGE1):c.211G>A (p.Glu71Lys)

gnomAD frequency: 0.00057  dbSNP: rs116164106
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000146258 SCV000193512 uncertain significance Muscular dystrophy 2013-12-05 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000710160 SCV000230242 uncertain significance not provided 2016-05-19 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000555307 SCV000438178 uncertain significance Muscular dystrophy-dystroglycanopathy type B6 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000379599 SCV000438179 uncertain significance Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
GeneDx RCV000710160 SCV000582521 uncertain significance not provided 2023-05-24 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 17878207, 25279699, 24709677)
Athena Diagnostics RCV000710160 SCV000613996 uncertain significance not provided 2017-09-27 criteria provided, single submitter clinical testing
Invitae RCV000555307 SCV000638993 uncertain significance Muscular dystrophy-dystroglycanopathy type B6 2022-10-13 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 71 of the LARGE1 protein (p.Glu71Lys). This variant is present in population databases (rs116164106, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with LARGE1-related conditions. ClinVar contains an entry for this variant (Variation ID: 158807). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV000765632 SCV000896960 uncertain significance Muscular dystrophy-dystroglycanopathy type B6; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1; Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A6 2018-10-31 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000710160 SCV001748040 uncertain significance not provided 2021-06-01 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000710160 SCV003816462 likely benign not provided 2023-06-29 criteria provided, single submitter clinical testing

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