ClinVar Miner

Submissions for variant NM_003978.5(PSTPIP1):c.247C>A (p.Gln83Lys)

dbSNP: rs377719165
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000757700 SCV000886022 uncertain significance not provided 2018-05-15 criteria provided, single submitter clinical testing The PSTPIP1 c.247C>A; p.Gln83Lys variant, to our knowledge, is not reported in the medical literature or in gene-specific databases. The variant is listed in the Genome Aggregation Database in 1 out of 246098 alleles, indicating it is not a common polymorphism. The glutamine at codon 83 is conserved across species but computational analyses (SIFT: Damaging, PolyPhen-2: Benign) predict conflicting effects of this variant on protein structure/function. Additionally, this variant occurs in the last nucleotide of the exon, a nucleotide generally conserved for the splicing mechanism. This nucleotide, however, is not well conserved and computational splicing algorithms also predict conflicting effects on splicing (Alamut v.2.11). Considering available information, the clinical significance of this variant cannot be determined with certainty. Pathogenic PSTPIP1 variants are causative for pyogenic sterile arthritis, pyoderma gangrenosum, and acne (PAPA syndrome, MIM: 604416).
Labcorp Genetics (formerly Invitae), Labcorp RCV001342468 SCV001536403 uncertain significance Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2020-05-13 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. 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"). This variant has not been reported in the literature in individuals with PSTPIP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 618851). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glutamine with lysine at codon 83 of the PSTPIP1 protein (p.Gln83Lys). The glutamine residue is highly conserved and there is a small physicochemical difference between glutamine and lysine.

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