ClinVar Miner

Submissions for variant NM_015559.3(SETBP1):c.79C>T (p.Pro27Ser)

dbSNP: rs751389887
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001913363 SCV002174795 uncertain significance not provided 2023-02-25 criteria provided, single submitter clinical testing This variant has not been reported in the literature in individuals affected with SETBP1-related conditions. 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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The serine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1402103). This variant is present in population databases (rs751389887, gnomAD 0.003%). This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 27 of the SETBP1 protein (p.Pro27Ser).
Ambry Genetics RCV002555633 SCV003559738 uncertain significance Inborn genetic diseases 2021-07-19 criteria provided, single submitter clinical testing The c.79C>T (p.P27S) alteration is located in exon 2 (coding exon 1) of the SETBP1 gene. This alteration results from a C to T substitution at nucleotide position 79, causing the proline (P) at amino acid position 27 to be replaced by a serine (S). Based on data from the Genome Aggregation Database (gnomAD), the SETBP1 c.79C>T alteration was observed in <0.01% (1/227,232) of total alleles studied. This amino acid position is not well conserved in available vertebrate species. The p.P27S alteration is predicted to be tolerated by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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