Submissions for variant NM_001172509.2(SATB2):c.1196G>A (p.Arg399His)

dbSNP: rs1057518190

Total submissions: 7

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
GeneDx	RCV000413401	SCV000491632	pathogenic	not provided	2023-02-01	criteria provided, single submitter	clinical testing	Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31021519, 25533962, 28151491, 28135719, 28191890, 31785789, 36457071)
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne	RCV000824998	SCV000966186	pathogenic	Chromosome 2q32-q33 deletion syndrome	2018-06-05	criteria provided, single submitter	clinical testing
Mendelics	RCV000824998	SCV001136132	pathogenic	Chromosome 2q32-q33 deletion syndrome	2019-05-28	criteria provided, single submitter	clinical testing
3billion, Medical Genetics	RCV000824998	SCV002318668	pathogenic	Chromosome 2q32-q33 deletion syndrome	2022-03-22	criteria provided, single submitter	clinical testing	Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000373069, PMID:28151491). The variant has been previously reported as de novo in a similarly affected individual (PMID: 25533962). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV001181946, PMID:31021519,28787087). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.994>=0.75). It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
Institute of Immunology and Genetics Kaiserslautern	RCV000824998	SCV005043007	likely pathogenic	Chromosome 2q32-q33 deletion syndrome	2024-04-25	criteria provided, single submitter	clinical testing	ACMG Criteria: PM2, PM5, PM1, PP5, BP4, PP1, PP4; Variant was found in heterozygous state
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000413401	SCV001808531	likely pathogenic	not provided		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000413401	SCV001954868	likely pathogenic	not provided		no assertion criteria provided	clinical testing