R239H (p.Arg239His) variant of ATL1 (Atlastin-1)
R239H (p.Arg239His) in ATL1 (Atlastin-1) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as likely pathogenic in the context of Spastic paraplegia; Hereditary spastic paraplegia 3A. The available variant effect predictions contribute to a CATVariant prioritization score of 0.60 / 1. The record also includes population frequency data, published literature, and structural context.
R239H (p.Arg239His) variant details
- p.Arg239His
- rs1241621325
- ClinGen CA389671154
- cosmic curated COSV63296
- ClinVar RCV001316506
- Likely pathogenic
- Spastic paraplegia; Hereditary spastic paraplegia 3A
- Missense
- Variant Prioritization Score for Impact Estimate 0.595
- REVEL 0.51
- AlphaMissense 0.91
- MetaLR 0.30
- MetaSVM -0.31
- CADD 25.90
- PolyPhen-2 0.80
- ClinVar: Likely pathogenic (Spastic paraplegia; Hereditary spastic paraplegia 3A)
- EBI: Pathogenic (in SPG3)
- UniProt: Pathogenic (in SPG3)
- Most common in the 1KG:CLM population (allele frequency 0.0053)
- Structural context available
- Cited in: Uncomplicated (Pure) Hereditary Spastic Paraplegia Overview. (PMID 20301682)
- Cited in: Spastic Paraplegia 3A. (PMID 20862796)