ClinVar Miner

Submissions for variant NM_001379110.1(SLC9A6):c.487G>A (p.Ala163Thr)

dbSNP: rs796053281
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Total submissions: 4
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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 RCV001051665 SCV001712040 uncertain significance Christianson syndrome 2023-08-28 reviewed by expert panel curation The p.Ala215Thr variant in SLC9A6 is absent from gnomAD (PM2_supporting). The p.Ala163Thr variant is observed in at least 1 unaffected individual (internal database) (BS2_Supporting). The p.Ala215Thr variant is found in a patient with an alternate molecular basis of disease (internal database) (BP5). In summary, the p.Ala215Thr variant in the SLC9A6 gene is classified as a Variant of Uncertain Significance based on the ACMG/AMP criteria (PM2_supporting, BS2_Supporting, BP5).
GeneDx RCV000189407 SCV000243046 likely benign not provided 2021-12-21 criteria provided, single submitter clinical testing See Variant Classification Assertion Criteria.
Labcorp Genetics (formerly Invitae), Labcorp RCV001051665 SCV001215833 uncertain significance Christianson syndrome 2020-02-22 criteria provided, single submitter clinical testing This sequence change replaces alanine with threonine at codon 183 of the SLC9A6 protein (p.Ala183Thr). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and threonine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with SLC9A6-related conditions. ClinVar contains an entry for this variant (Variation ID: 207239). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000189407 SCV004225684 uncertain significance not provided 2023-05-05 criteria provided, single submitter clinical testing BP5, PM2

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