ClinVar Miner

Submissions for variant NM_003978.5(PSTPIP1):c.1183G>A (p.Gly395Ser)

gnomAD frequency: 0.00002  dbSNP: rs142544259
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001059383 SCV001224007 uncertain significance Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2022-11-09 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PSTPIP1 protein function. ClinVar contains an entry for this variant (Variation ID: 854353). This variant has not been reported in the literature in individuals affected with PSTPIP1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 395 of the PSTPIP1 protein (p.Gly395Ser).
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001059383 SCV001468469 uncertain significance Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2021-03-30 criteria provided, single submitter clinical testing PSTPIP1 NM_003978.4 exon 15 p.Gly395Ser (c.1183G>A): This variant has not been reported in the literature but is present in 0.04% (9/19522) of East Asian alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/15-77329449-G-A?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:854353). Evolutionary conservation suggests that this variant may impact the protein; computational predictive tools are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Ambry Genetics RCV002554419 SCV003713028 uncertain significance Inborn genetic diseases 2021-06-22 criteria provided, single submitter clinical testing The c.1183G>A (p.G395S) alteration is located in exon 15 (coding exon 15) of the PSTPIP1 gene. This alteration results from a G to A substitution at nucleotide position 1183, causing the glycine (G) at amino acid position 395 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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