ClinVar Miner

Submissions for variant NM_003978.5(PSTPIP1):c.59C>T (p.Thr20Met) (rs553718554)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000299645 SCV000393987 likely benign Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Invitae RCV000299645 SCV000932754 uncertain significance Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2020-04-17 criteria provided, single submitter clinical testing This sequence change replaces threonine with methionine at codon 20 of the PSTPIP1 protein (p.Thr20Met). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and methionine. This variant is present in population databases (rs553718554, ExAC 0.2%). This variant has not been reported in the literature in individuals with PSTPIP1-related disease. ClinVar contains an entry for this variant (Variation ID: 317170). 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.

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