ClinVar Miner

Submissions for variant NM_004782.4(SNAP29):c.354dup (p.Leu119fs) (rs751575036)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000280604 SCV000329589 pathogenic not provided 2017-11-09 criteria provided, single submitter clinical testing The c.354dupG pathogenic variant in the SNAP29 gene has been reported previously in the homozygous state on clinical exome sequencing, but phenotypic information was not provided on the proband (Farwell et al., 2015). The c.354dupG variant causes a frameshift starting with codon Leucine 119, changes this amino acid to a Alanine residue, and creates a premature Stop codon at position 15 of the new reading frame, denoted p.Leu119AlafsX15. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.354dupG variant is observed in 5/33,582 (0.015%) alleles from individuals of Latino background in large population cohorts (Lek et al., 2016). We interpret c.354dupG as a pathogenic variant.
Illumina Clinical Services Laboratory,Illumina RCV000778648 SCV000914980 uncertain significance CEDNIK syndrome 2018-11-08 criteria provided, single submitter clinical testing The SNAP29 c.354dupG (p.Leu119AlafsTer15) variant results in a frameshift and is predicted to cause a premature truncation of the protein. The p.Leu119AlafsTer15 variant has been reported in one study, in which it is found in a homozygous state in an individual with an undiagnosed disorder (Farwell et al. 2015). This variant is not found in the 1000 Genomes Project, the Exome Sequencing Project, Exome Aggregation Consortium, or the Genome Aggregation Database in a region of good sequence coverage so the variant is presumed to be rare. Due to the potential impact of frameshift variants and the lack of clarifying evidence, this variant is classified as a variant of unknown significance but suspicious for pathogenicity for cerebral dysgenesis, neuropathy, ichthyosis, and palmoplantar keratoderma syndrome. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.
New York Genome Center RCV000778648 SCV001480323 likely pathogenic CEDNIK syndrome 2019-09-13 criteria provided, single submitter clinical testing
Tgen's Center For Rare Childhood Disorders,Translational Genomics Research Institute (TGEN) RCV000454232 SCV000538078 pathogenic Leukodystrophy, hypomyelinating, 2 2017-02-06 no assertion criteria provided clinical testing

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