ClinVar Miner

Submissions for variant NM_001378778.1(MPDZ):c.1735C>T (p.Arg579Ter)

gnomAD frequency: 0.00001  dbSNP: rs571799365
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001571162 SCV001795581 pathogenic not provided 2022-01-14 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed at a significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge
DASA RCV002221632 SCV002499404 pathogenic Hydrocephalus, nonsyndromic, autosomal recessive 2 2022-04-10 criteria provided, single submitter clinical testing The c.1735C>T;p.(Arg579*) variant creates a premature translational stop signal in the MPDZ gene. It is expected to result in an absent or disrupted protein product -PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 1204727) - PS4_supporting. The variant is present at low allele frequencies population databases (rs571799365 – gnomAD 0.0001316%; ABraOM no frequency - https://abraom.ib.usp.br/) - PM2_supporting. In summary, the currently available evidence indicates that the variant is pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001571162 SCV002962347 pathogenic not provided 2023-08-17 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 1204727). This variant has not been reported in the literature in individuals affected with MPDZ-related conditions. This variant is present in population databases (rs571799365, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Arg579*) in the MPDZ gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MPDZ are known to be pathogenic (PMID: 23240096, 28556411).

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