ClinVar Miner

Submissions for variant NM_003978.5(PSTPIP1):c.1054G>A (p.Glu352Lys) (rs201186216)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000269627 SCV000394012 benign Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
GeneDx RCV000497366 SCV000589351 likely benign not specified 2017-12-18 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Invitae RCV000269627 SCV000764078 likely benign Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2020-11-04 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000269627 SCV001472995 uncertain significance Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2020-03-10 criteria provided, single submitter clinical testing The PSTPIP1 c.1054G>A; p.Glu352Lys variant (rs201186216), to our knowledge, is not reported in the medical literature, but is reported in a database in an individual with an autoinflammatory disease (see link below). The variant is reported in the ClinVar database (Variation ID: 317183) and in the general population with an allele frequency of 0.03% (83/277034 alleles) in the Genome Aggregation database. The amino acid at this position is weakly conserved and computational algorithms (PolyPhen-2, SIFT) predict this variant is tolerated. Due to limited information, the clinical significance of this variant is uncertain. References: Link to Infevers database: https://infevers.umai-montpellier.fr/web/search.php?n=5

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