ClinVar Miner

Submissions for variant NM_015166.4(MLC1):c.76G>A (p.Ala26Thr)

gnomAD frequency: 0.00021  dbSNP: rs201522059
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000901502 SCV001045876 likely benign not provided 2024-12-02 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005408058 SCV006072458 likely benign not specified 2025-03-19 criteria provided, single submitter clinical testing Variant summary: MLC1 c.76G>A (p.Ala26Thr) 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 0.00054 in 250670 control chromosomes, predominantly at a frequency of 0.0036 within the Latino subpopulation in the gnomAD database. The observed variant frequency within Latino control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in MLC1 causing Megalencephalic Leukoencephalopathy With Subcortical Cysts 1 phenotype (0.0011). To our knowledge, no occurrence of c.76G>A in individuals affected with Megalencephalic Leukoencephalopathy With Subcortical Cysts 1 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 727189). Based on the evidence outlined above, the variant was classified as likely benign.
Natera, Inc. RCV001274277 SCV001458248 likely benign Megalencephalic leukoencephalopathy with subcortical cysts 2020-09-16 no assertion criteria provided clinical testing
PreventionGenetics, part of Exact Sciences RCV003958148 SCV004769887 likely benign MLC1-related disorder 2023-01-12 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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