Submissions for variant NM_005862.3(STAG1):c.2936A>G (p.Lys979Arg)

gnomAD frequency: 0.00001  dbSNP: rs1471479119

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Johns Hopkins Genomics, Johns Hopkins University	RCV001007612	SCV001167299	likely pathogenic	Intellectual disability, autosomal dominant 47	2019-11-11	criteria provided, single submitter	clinical testing	This variant (rs1471479119) has been previously reported in a four year-old female with developmental delay and various dysmoprhic features, for whom parental studies confirmed that this variant was de novo. Additionally, this variant is absent from a large population dataset and a single submitter in ClinVar classifies this variant as likely pathogenic. c.2936A>G alters the last nucleotide of STAG1 exon 27. Bioinformatic analysis predicts that this missense variant may increase the strength of the intron 27 splice donor site although this has not been confirmed experimentally to our knowledge. Three bioinformatic tools queried predict that this substitution would be tolerated, but the lysine residue at this position is evolutionarily conserved across all but one species assessed. We consider this variant to be likely pathogenic.
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	RCV000506168	SCV000605730	likely pathogenic	STAG1-related disorder	2016-12-20	no assertion criteria provided	clinical testing
GenomeConnect - Brain Gene Registry	RCV001007612	SCV004176869	not provided	Intellectual disability, autosomal dominant 47		no assertion provided	phenotyping only	Variant classified as Likely pathogenic and reported on 11-12-2019 by John Hopkins Genomics DNA Diagnostic Laboratory. Assertions are reported exactly as they appear on the patient provided laboratory report. GenomeConnect does not attempt to reinterpret the variant. The IDDRC-CTSA National Brain Gene Registry (BGR) is a study funded by the U.S. National Center for Advancing Translational Sciences (NCATS) and includes 13 Intellectual and Developmental Disability Research Center (IDDRC) institutions. The study is led by Principal Investigator Dr. Philip Payne from Washington University. The BGR is a data commons of gene variants paired with subject clinical information. This database helps scientists learn more about genetic changes and their impact on the brain and behavior. Participation in the Brain Gene Registry requires participation in GenomeConnect. More information about the Brain Gene Registry can be found on the study website - https://braingeneregistry.wustl.edu/.