ClinVar Miner

Submissions for variant NM_000426.3(LAMA2):c.6161A>G (p.Gln2054Arg) (rs56035053)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000178515 SCV000230610 uncertain significance not provided 2015-02-16 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000192788 SCV000247812 uncertain significance not specified 2015-04-05 criteria provided, single submitter clinical testing
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000178515 SCV000280638 uncertain significance not provided 2015-09-29 criteria provided, single submitter clinical testing Converted during submission to Uncertain significance.
PreventionGenetics,PreventionGenetics RCV000192788 SCV000304170 benign not specified criteria provided, single submitter clinical testing
Fulgent Genetics,Fulgent Genetics RCV000509541 SCV000611393 uncertain significance Merosin deficient congenital muscular dystrophy 2017-05-23 criteria provided, single submitter clinical testing
Invitae RCV000549092 SCV000658733 uncertain significance Laminin alpha 2-related dystrophy 2020-01-02 criteria provided, single submitter clinical testing This sequence change replaces glutamine with arginine at codon 2054 of the LAMA2 protein (p.Gln2054Arg). The glutamine residue is moderately conserved and there is a small physicochemical difference between glutamine and arginine. This variant is present in population databases (rs56035053, ExAC 0.1%). This variant has not been reported in the literature in individuals with LAMA2-related disease. ClinVar contains an entry for this variant (Variation ID: 197478). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The arginine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Athena Diagnostics Inc RCV000178515 SCV000842624 uncertain significance not provided 2017-11-24 criteria provided, single submitter clinical testing
GeneDx RCV000178515 SCV000980463 likely benign not provided 2018-05-22 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Illumina Clinical Services Laboratory,Illumina RCV001154910 SCV001316304 uncertain significance Congenital muscular dystrophy due to partial LAMA2 deficiency 2018-01-13 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.
GenomeConnect, ClinGen RCV000509541 SCV000606884 not provided Merosin deficient congenital muscular dystrophy no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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