P499A (p.Pro499Ala) variant of SHMT2 (P34897)
P499A (p.Pro499Ala) in SHMT2 (P34897) is a missense change. Clinical records from ClinVar, EBI, and UniProt describe it as likely pathogenic in the context of Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormali. The available variant effect predictions contribute to a CATVariant prioritization score of 0.68 / 1. The record also includes population frequency data, published literature, and structural context.
P499A (p.Pro499Ala) variant details
- p.Pro499Ala
- rs2037465152
- ClinGen CA385406054
- ClinVar RCV001270311
- UniProt VAR 085471
- Likely pathogenic
- Neurodevelopmental disorder with cardiomyopathy, spasticity, and brain abnormali
- Missense
- Variant Prioritization Score for Impact Estimate 0.683
- REVEL 0.61
- CADD 25.30
- PolyPhen-2 0.99
- SIFT 0.01
- ClinVar: Likely pathogenic (Neurodevelopmental disorder with cardiomyopathy, spasticity, and)
- EBI: Pathogenic (in NEDCASB)
- UniProt: Pathogenic (in NEDCASB)
- Most common in the REMAINING population (allele frequency 0.00048)
- Structural context available
- Cited in: Impairment of the mitochondrial one-carbon metabolism enzyme SHMT2 causes a novel brain and heart developmental… (PMID 33015733)