E5Q (p.Glu5Gln) variant of PMS2 (P54278)
E5Q (p.Glu5Gln) in PMS2 (P54278) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as conflicting interpretations in the context of Hereditary nonpolyposis colorectal neoplasms; not specified; Hereditary cancer-p. The available variant effect predictions contribute to a CATVariant prioritization score of 0.43 / 1. The record also includes population frequency data, published literature, and structural context.
E5Q (p.Glu5Gln) variant details
- p.Glu5Gln
- rs372539944
- ClinGen CA043392
- NCI-TCGA Cosmic COSV5614
- cosmic curated COSV56152
- Conflicting interpretations
- Hereditary nonpolyposis colorectal neoplasms; not specified; Hereditary cancer-p
- Missense
- Variant Prioritization Score for Impact Estimate 0.427
- REVEL 0.33
- AlphaMissense 0.17
- MetaLR 0.60
- MetaSVM -0.45
- CADD 20.60
- PolyPhen-2 0.68
- ClinVar: Conflicting classifications of pathogenicity (Hereditary nonpolyposis colorectal neoplasms; not specified; Her)
- EBI: Benign
- UniProt: Benign
- Most common in the African/African-American population (allele frequency 2.8e-05)
- Structural context available
- Cited in: A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic… (PMID 25394175)
- Cited in: Practice parameters for the identification and testing of patients at risk for dominantly inherited colorectal… (PMID 11598466)