ClinVar Miner

Submissions for variant NM_000426.4(LAMA2):c.6429+1G>T

gnomAD frequency: 0.00002  dbSNP: rs1262029350
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001041706 SCV001205336 pathogenic LAMA2-related muscular dystrophy 2024-12-03 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 45 of the LAMA2 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in LAMA2 are known to be pathogenic (PMID: 18700894, 32904964). This variant is present in population databases (no rsID available, gnomAD 0.004%). Disruption of this splice site has been observed in individual(s) with congenital muscular dystrophy (PMID: 30055037). ClinVar contains an entry for this variant (Variation ID: 556858). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001784278 SCV002016418 pathogenic not provided 2022-07-13 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV001810478 SCV002060301 pathogenic Merosin deficient congenital muscular dystrophy; Muscular dystrophy, limb-girdle, autosomal recessive 23 2021-11-16 criteria provided, single submitter clinical testing NM_000426.3(LAMA2):c.6429+1G>T is a canonical splice variant classified as pathogenic in the context of muscular dystrophy, LAMA2-related. c.6429+1G>T has been observed in cases with relevant disease (PMID: 30055037). Functional assessments of this variant are not available in the literature. c.6429+1G>T has been observed in population frequency databases (gnomAD: NFE <0.001%). In summary, NM_000426.3(LAMA2):c.6429+1G>T is a canonical splice variant in a gene where loss of function is a known mechanism of disease, is predicted to disrupt protein function, and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center RCV001810478 SCV002061808 likely pathogenic Merosin deficient congenital muscular dystrophy; Muscular dystrophy, limb-girdle, autosomal recessive 23 2021-12-30 criteria provided, single submitter clinical testing PVS1, PM2
Fulgent Genetics, Fulgent Genetics RCV001810478 SCV002781039 pathogenic Merosin deficient congenital muscular dystrophy; Muscular dystrophy, limb-girdle, autosomal recessive 23 2021-10-17 criteria provided, single submitter clinical testing
Baylor Genetics RCV003465520 SCV004190510 likely pathogenic Merosin deficient congenital muscular dystrophy 2023-05-12 criteria provided, single submitter clinical testing

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