ClinVar Miner

Submissions for variant NM_001080517.3(SETD5):c.3301C>T (p.Gln1101Ter)

dbSNP: rs1304648449
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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 RCV001956437 SCV002247302 pathogenic not provided 2020-12-18 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with SETD5-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln1101*) in the SETD5 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in SETD5 are known to be pathogenic (PMID: 24680889).
Ambry Genetics RCV004970649 SCV005495717 pathogenic Inborn genetic diseases 2024-09-27 criteria provided, single submitter clinical testing The c.3301C>T (p.Q1101*) alteration, located in exon 20 (coding exon 18) of the SETD5 gene, consists of a C to T substitution at nucleotide position 3301. This changes the amino acid from a glutamine (Q) to a stop codon at amino acid position 1101. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This nucleotide position is highly conserved in available vertebrate species. RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). In silico splice site analysis predicts that this alteration will result in the creation or strengthening of a novel splice donor site. Based on the available evidence, this alteration is classified as pathogenic.

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