ClinVar Miner

Submissions for variant NM_001172509.2(SATB2):c.1660G>A (p.Val554Ile)

gnomAD frequency: 0.00003  dbSNP: rs1201673032
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000704967 SCV000833943 uncertain significance Chromosome 2q32-q33 deletion syndrome 2023-05-21 criteria provided, single submitter clinical testing In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is not expected to disrupt SATB2 function. ClinVar contains an entry for this variant (Variation ID: 581209). This variant has not been reported in the literature in individuals affected with SATB2-related conditions. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 554 of the SATB2 protein (p.Val554Ile).
GeneDx RCV001766553 SCV001990903 uncertain significance not provided 2019-04-03 criteria provided, single submitter clinical testing In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV004026676 SCV004943320 likely benign Inborn genetic diseases 2023-09-26 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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