ClinVar Miner

Submissions for variant NM_001379110.1(SLC9A6):c.-56-25C>G

gnomAD frequency: 0.00002  dbSNP: rs782396686
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel RCV001857654 SCV004808299 likely benign Christianson syndrome 2024-02-23 reviewed by expert panel curation The p.Arg26Gly variant in SLC9A6 (NM_006359.2) is present in 2 XX and 1 XY individual(s) in gnomAD v2 (0.004%) (not sufficient to meet BS1 criteria). The p.Arg26Gly variant is observed in the hemizygous state in at least 2 unaffected individuals (internal database - GeneDx) (BS2). The p.Arg26Gly variant is found in a patient with an alternate molecular basis of disease (internal database -GeneDx) (BP5). Computational analysis prediction tools suggest that the p.Arg26Gly variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Arg26Gly variant in SLC9A6 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP5, BP4).
GeneDx RCV000189404 SCV000243043 likely benign not specified 2014-03-10 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Labcorp Genetics (formerly Invitae), Labcorp RCV001857654 SCV002165760 uncertain significance Christianson syndrome 2023-11-10 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 26 of the SLC9A6 protein (p.Arg26Gly). This variant is present in population databases (rs782396686, gnomAD 0.004%), including at least one homozygous and/or hemizygous individual. This variant has not been reported in the literature in individuals affected with SLC9A6-related conditions. ClinVar contains an entry for this variant (Variation ID: 207236). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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.

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