A15T (p.Ala15Thr) variant of MSH2 (DNA mismatch repair protein Msh2)
A15T (p.Ala15Thr) in MSH2 (DNA mismatch repair protein Msh2) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as conflicting interpretations in the context of Hereditary cancer-predisposing syndrome; not provided; Lynch syndrome 1. The available variant effect predictions contribute to a CATVariant prioritization score of 0.50 / 1. The record also includes population frequency data, published literature, and structural context.
A15T (p.Ala15Thr) variant details
- p.Ala15Thr
- rs1183892581
- ClinGen CA346728542
- ClinVar RCV000630170
- ClinVar RCV001764503
- Conflicting interpretations
- Hereditary cancer-predisposing syndrome; not provided; Lynch syndrome 1
- Missense
- Variant Prioritization Score for Impact Estimate 0.498
- REVEL 0.45
- ESM-1b 0.41
- AlphaMissense 0.12
- MetaLR 0.63
- MetaSVM 0.16
- CADD 22.90
- ClinVar: Conflicting classifications of pathogenicity (Hereditary cancer-predisposing syndrome; not provided; Lynch syn)
- EBI: Likely benign
- UniProt: Likely benign
- Most common in the 1KG:PUR population (allele frequency 0.0051)
- 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)