ClinVar Miner

Submissions for variant NM_001080517.3(SETD5):c.2003C>G (p.Ser668Ter)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
MGZ Medical Genetics Center RCV002290370 SCV002580475 likely pathogenic Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency 2021-07-15 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV003101674 SCV003011717 pathogenic not provided 2022-03-27 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with SETD5-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Ser668*) 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).
Laboratoire de Génétique Moléculaire, CHU Bordeaux RCV002290370 SCV003836671 pathogenic Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency 2019-10-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV003365729 SCV004070106 pathogenic Inborn genetic diseases 2023-07-17 criteria provided, single submitter clinical testing The c.2003C>G (p.S668*) alteration, located in exon 15 (coding exon 13) of the SETD5 gene, consists of a C to G substitution at nucleotide position 2003. This changes the amino acid from a serine (S) to a stop codon at amino acid position 668. 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 variant has been reported as de novo in an individual with features consistent with SETD5-related neurodevelopmental disorder (Arteche-López, 2021). Based on the available evidence, this alteration is classified as pathogenic.

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