ClinVar Miner

Submissions for variant NM_003978.5(PSTPIP1):c.-123G>A

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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 RCV001286292 SCV001472837 likely benign Pyogenic arthritis-pyoderma gangrenosum-acne syndrome 2020-03-23 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001355682 SCV001550636 uncertain significance not provided no assertion criteria provided clinical testing The PSTPIP1 p.Ala25Thr variant was not identified in the literature nor was it identified in ClinVar or LOVD 3.0. The variant was identified in dbSNP (ID: rs771172891) and in control databases in 16 of 180202 chromosomes at a frequency of 0.000089 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: Other in 2 of 4714 chromosomes (freq: 0.000424), Latino in 8 of 25630 chromosomes (freq: 0.000312) and European (non-Finnish) in 6 of 80246 chromosomes (freq: 0.000075), but was not observed in the African, Ashkenazi Jewish, East Asian, European (Finnish), and South Asian populations. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Ala25 residue is not conserved in mammals and 3 of 4 computational analyses (PolyPhen-2, AlignGVGD, BLOSUM, MutationTaster) do not predict an impact to the protein. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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