ClinVar Miner

Submissions for variant NM_001077365.2(POMT1):c.1196del (p.Leu399fs)

gnomAD frequency: 0.00002  dbSNP: rs768144522
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV001093194 SCV001250052 pathogenic not provided 2017-10-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002554865 SCV003564798 pathogenic Inborn genetic diseases 2021-04-29 criteria provided, single submitter clinical testing The c.1262delT (p.L421Rfs*29) alteration, located in exon 13 (coding exon 12) of the POMT1 gene, consists of a deletion of one nucleotide at position 1262, causing a translational frameshift with a predicted alternate stop codon after 29 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from the Genome Aggregation Database (gnomAD) database, the POMT1 c.1262delT alteration was observed in 0.002% (5/251,494) of total alleles studied, with a frequency of 0.02% (5/30,616) in the South Asian subpopulation. Based on the available evidence, this alteration is classified as pathogenic.
Baylor Genetics RCV003473715 SCV004204050 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A1 2024-03-26 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003769027 SCV004595934 pathogenic Autosomal recessive limb-girdle muscular dystrophy type 2K; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B1; Walker-Warburg congenital muscular dystrophy 2023-10-24 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu421Argfs*29) in the POMT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in POMT1 are known to be pathogenic (PMID: 12369018, 15637732, 16575835). This variant is present in population databases (rs768144522, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with POMT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 872615). For these reasons, this variant has been classified as Pathogenic.

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