ClinVar Miner

Submissions for variant NM_001242908.2(RSPO1):c.115G>A (p.Ala39Thr)

dbSNP: rs201499112
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001934152 SCV002213035 uncertain significance not provided 2022-06-13 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 39 of the RSPO1 protein (p.Ala39Thr). This variant is present in population databases (rs201499112, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with RSPO1-related conditions. 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: "Benign"; 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.
Fulgent Genetics, Fulgent Genetics RCV002503673 SCV002783483 uncertain significance Palmoplantar keratoderma-XX sex reversal-predisposition to squamous cell carcinoma syndrome 2022-04-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV004043014 SCV005013815 uncertain significance Inborn genetic diseases 2023-09-26 criteria provided, single submitter clinical testing The c.115G>A (p.A39T) alteration is located in exon 5 (coding exon 2) of the RSPO1 gene. This alteration results from a G to A substitution at nucleotide position 115, causing the alanine (A) at amino acid position 39 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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