ClinVar Miner

Submissions for variant NM_001080517.3(SETD5):c.2279C>A (p.Ser760Ter)

dbSNP: rs1553626575
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 2
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000657788 SCV000779541 pathogenic not provided 2018-05-14 criteria provided, single submitter clinical testing The S760X variant in the SETD5 gene has not been reported previously as a pathogenic variant nor as a benign variant to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The S760X variant is not observed in large population cohorts (Lek et al., 2016). We interpret S760X as a pathogenic variant.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002272317 SCV002557637 pathogenic Intellectual disability-facial dysmorphism syndrome due to SETD5 haploinsufficiency 2022-02-02 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with SETD5-related intellectual disability (MIM#615761). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. There are at least ten previously reported likely pathogenic or pathogenic NMD-predicted variants (Decipher, ClinVar). (SP) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant has been classified once as pathogenic by a clinical diagnostic laboratory (ClinVar). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.