ClinVar Miner

Submissions for variant NM_001172509.2(SATB2):c.1696G>A (p.Glu566Lys)

dbSNP: rs1064795530
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000482629 SCV000571436 pathogenic not provided 2024-07-22 criteria provided, single submitter clinical testing Published functional studies suggest this variant impairs interaction with chromatin, however additional studies are needed to validate the functional effect of this variant in vivo (PMID: 28151491); In silico analysis indicates that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28151491, 33057194, 35982159, 35241104)
Labcorp Genetics (formerly Invitae), Labcorp RCV000656509 SCV003525185 pathogenic Chromosome 2q32-q33 deletion syndrome 2022-08-31 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 422062). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects SATB2 function (PMID: 28151491). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SATB2 protein function. This missense change has been observed in individual(s) with clinical features of SATB2-related conditions (PMID: 28151491). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 566 of the SATB2 protein (p.Glu566Lys).
OMIM RCV000656509 SCV000778506 pathogenic Chromosome 2q32-q33 deletion syndrome 2018-06-15 no assertion criteria provided literature only

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