ClinVar Miner

Submissions for variant NM_013382.7(POMT2):c.248+1G>C

gnomAD frequency: 0.00001  dbSNP: rs961440747
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000702634 SCV000831495 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B2; Autosomal recessive limb-girdle muscular dystrophy type 2N 2023-02-06 criteria provided, single submitter clinical testing Disruption of this splice site has been observed in individual(s) with congenital muscular dystrophy (Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This sequence change affects a donor splice site in intron 1 of the POMT2 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 POMT2 are known to be pathogenic (PMID: 15894594). This variant is present in population databases (no rsID available, gnomAD 0.002%). ClinVar contains an entry for this variant (Variation ID: 579369). 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.
Baylor Genetics RCV003472239 SCV004204124 likely pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A2 2024-03-06 criteria provided, single submitter clinical testing

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