ClinVar Miner

Submissions for variant NM_019066.5(MAGEL2):c.1912C>T (p.Gln638Ter)

dbSNP: rs797044883
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 11
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000190699 SCV000244140 pathogenic Inborn genetic diseases 2014-09-03 criteria provided, single submitter clinical testing
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000238706 SCV000297290 likely pathogenic not provided 2015-12-03 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000762935 SCV000893358 pathogenic Prader-Willi syndrome; Schaaf-Yang syndrome 2018-10-31 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000508676 SCV001158491 pathogenic Schaaf-Yang syndrome 2019-06-26 criteria provided, single submitter clinical testing
Center for Molecular Medicine, Children’s Hospital of Fudan University RCV000508676 SCV001622604 pathogenic Schaaf-Yang syndrome 2021-05-19 criteria provided, single submitter clinical testing
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000508676 SCV002012480 pathogenic Schaaf-Yang syndrome 2021-10-13 criteria provided, single submitter research ACMG codes: PVS1; PS4M; PM2; PP5
PreventionGenetics, part of Exact Sciences RCV003407693 SCV004112089 pathogenic MAGEL2-related disorder 2023-04-20 criteria provided, single submitter clinical testing The MAGEL2 c.1912C>T variant is predicted to result in premature protein termination (p.Gln638*). This variant was reported in multiple individuals with Schaaf-Yang syndrome and de novo occurrences have been noted in several cases (Urreizti et al. 2017. PubMed ID: 28281571; Halloun et al. 2021. PubMed ID: 34051361; Negishi et al. 2019. PubMed ID: 31791363). This variant was also reported in a patient with neonatal demise (Yang et al. 2019. PubMed ID: 31501239). This variant has not been reported in a large population database (, indicating this variant is rare. This variant has been interpreted as pathogenic and likely pathogenic by multiple submitters in ClinVar ( Nonsense variants in MAGEL2 are expected to be pathogenic. This variant is interpreted as pathogenic.
GeneDx RCV000238706 SCV004170148 pathogenic not provided 2023-10-08 criteria provided, single submitter clinical testing Nonsense variant predicted to result in protein truncation, as the last 612 amino acids are lost, and other loss-of-function variants have been reported downstream in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27195816, 31501239, 28281571, 31791363, 29359444, 34128869, 35595280, 34051361, 37404980, 33726816, 36243518)
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center RCV000508676 SCV004809925 pathogenic Schaaf-Yang syndrome 2024-04-04 criteria provided, single submitter clinical testing
OMIM RCV000508676 SCV000605831 pathogenic Schaaf-Yang syndrome 2017-09-26 no assertion criteria provided literature only
Department Of Pediatrics And Neonatology, Nagoya City University Graduate School Of Medical Sciences RCV000508676 SCV000784667 pathogenic Schaaf-Yang syndrome 2018-06-25 no assertion criteria provided clinical testing

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.