ClinVar Miner

Submissions for variant NM_020680.4(SCYL1):c.526A>T (p.Lys176Ter)

gnomAD frequency: 0.00003  dbSNP: rs535912271
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV000853313 SCV000996160 pathogenic Acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome 2018-06-27 criteria provided, single submitter clinical testing This nonsense variant found in exon 4 of 18 is predicted to result in loss of normal protein function. Loss of function variants are an established mechanism for disease in SCYL1. This variant has not been previously reported or functionally characterized in the literature to our knowledge. It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.526A>T (p.Lys176Ter) variant is predicted by multiple in silico tools to have a deleterious effect on protein function. This variant was detected in trans with a pathogenic variant. Based on the available evidence, the c.526A>T (p.Lys176Ter) variant is classified as pathogenic.
PreventionGenetics, part of Exact Sciences RCV003424376 SCV004107051 likely pathogenic SCYL1-related disorder 2022-10-02 criteria provided, single submitter clinical testing The SCYL1 c.526A>T variant is predicted to result in premature protein termination (p.Lys176*). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in SCYL1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

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