BPNT1
Chr 13'(2'), 5'-bisphosphate nucleotidase 1
Also known as: HEL20, HsPIP, PIP
BPNT1 encodes a phosphatase that converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP and hydrolyzes inositol 1,4-bisphosphate to inositol 4-phosphate, preventing toxic accumulation of PAP and participating in inositol recycling. Mutations cause autosomal recessive pontocerebellar hypoplasia type 1F, characterized by progressive microcephaly, intellectual disability, and cerebellar atrophy with onset in infancy or early childhood. The gene shows very low constraint against loss-of-function variants (pLI < 0.001), consistent with autosomal recessive inheritance.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
The highest-scoring mechanism for this gene is dominant-negative.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
BPNT1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools