ClinVar Miner

Submissions for variant NM_001281463.1(SMC1A):c.1429C>T (p.Arg477Ter) (rs1556890135)

Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000578696 SCV000681217 likely pathogenic not provided 2017-11-30 criteria provided, single submitter clinical testing The R499X nonsense variant in the SMC1A gene is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The variant is not observed in large population cohorts (Lek et al., 2016).
Illumina Clinical Services Laboratory,Illumina RCV001270901 SCV001451682 pathogenic SMC1A-related cohesinopathy 2019-05-01 criteria provided, single submitter clinical testing The SMC1A c.1495C>T (p.Arg499Ter) variant is a stop-gained variant that is predicted to result in an absent or truncated protein. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. The p.Arg499Ter variant is not found in the Genome Aggregation Database despite being located in a region of good sequencing coverage. Based on the potential impact of stop-gained variants in relation to the known mechanism of disease and the variant’s identification in a de novo state and its rarity, the p.Arg499Ter variant is classified as pathogenic for SMC1A-related cohesinopathy.
Invitae RCV001387822 SCV001588541 pathogenic Congenital muscular hypertrophy-cerebral syndrome 2020-10-09 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg499*) in the SMC1A gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with SMC1A-related conditions (PMID: 31098032, 31334757). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 489224). Loss-of-function variants in SMC1A are known to be pathogenic (PMID: 26386245, 27334371, 28166369, 28548707, 31334757). For these reasons, this variant has been classified as Pathogenic.

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.