ClinVar Miner

Submissions for variant NM_014254.3(RXYLT1):c.1064_1091del (p.Asp355fs)

gnomAD frequency: 0.00001  dbSNP: rs397514545
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001196501 SCV001367109 pathogenic not provided 2020-01-27 criteria provided, single submitter clinical testing This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PM2,PP5.
Invitae RCV001196501 SCV004552575 likely pathogenic not provided 2023-12-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Asp355Valfs*33) in the RXYLT1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 89 amino acid(s) of the RXYLT1 protein. This variant is present in population databases (rs397514545, gnomAD 0.0009%). This premature translational stop signal has been observed in individual(s) with cobblestone lissencephaly (PMID: 23217329). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 39606). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
OMIM RCV000032806 SCV000056574 pathogenic Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 10 2012-12-07 no assertion criteria provided literature only

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