Y1589C (p.Tyr1589Cys) variant of SCN2A (Nav1.2)
Y1589C (p.Tyr1589Cys) in SCN2A (Nav1.2) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as pathogenic/likely pathogenic in the context of Seizures, benign familial infantile, 3; Seizures, benign familial infantile, 5. The available variant effect predictions contribute to a CATVariant prioritization score of 0.83 / 1. The record also includes population frequency data, published literature, and structural context.
Y1589C (p.Tyr1589Cys) variant details
- p.Tyr1589Cys
- rs1553463119
- ClinGen CA349036779
- ClinVar RCV000548002
- ClinVar RCV000857242
- Pathogenic/Likely pathogenic
- Seizures, benign familial infantile, 3; Seizures, benign familial infantile, 5
- Missense
- Variant Prioritization Score for Impact Estimate 0.829
- REVEL 0.93
- ESM-1b 1.00
- AlphaMissense 0.95
- CADD 25.40
- PolyPhen-2 0.98
- SIFT 0.00
- ClinVar: Pathogenic/Likely pathogenic (Seizures, benign familial infantile, 3; Seizures, benign familia)
- EBI: Pathogenic (in BFIS3)
- UniProt: Pathogenic (in BFIS3)
- Most common in the African/African-American population (allele frequency 6e-05)
- Structural context available
- Cited in: An SCN2A mutation in a family with infantile seizures from Madagascar reveals an increased subthreshold Na(+) current. (PMID 23758435)
- Cited in: EFNS guidelines on the molecular diagnosis of channelopathies, epilepsies, migraine, stroke, and dementias. (PMID 20298421)