BPNT1: Bisphosphate 3'-Nucleotidase 1
A key regulator of inositol phosphate and sulfate metabolism, implicated in developmental and neurological disorders.
Gene Information Card
| Symbol | BPNT1 |
|---|---|
| Full Name | Bisphosphate 3'-Nucleotidase 1 |
| Gene Type | Protein coding |
| Chromosomal Location | 1q41 |
| NCBI Gene ID | 10380 ncbi.nlm.nih.gov/gene/10380 |
| Ensembl ID | ENSG00000162813 |
| UniProt ID | O95861 |
| OMIM ID | 606832 |
| HGNC ID | 1097 |
| Aliases | BPNT, HEL20, PAP-inositol phosphatase, 3'(2'),5'-bisphosphate nucleotidase 1 |
Description
BPNT1 encodes bisphosphate 3'-nucleotidase 1, an enzyme that catalyzes the dephosphorylation of 3'-phosphoadenosine 5'-phosphate (PAP) and inositol 1,4-bisphosphate (Ins(1,4)P2). This activity is essential for sulfate activation and inositol phosphate signaling. Mutations in BPNT1 are associated with developmental delay, intellectual disability, and skeletal abnormalities.
Disease Associations
| Disease category | Pathophysiological mechanism | Genomic evidence |
|---|---|---|
| Developmental and epileptic encephalopathy 104 (DEE104) | Loss-of-function mutations impair PAP phosphatase activity, disrupting sulfate metabolism and inositol signaling in neurons. | ClinVar, OMIM |
| Intellectual disability, autosomal recessive 73 (MRT73) | Homozygous missense variants reduce enzyme stability and catalytic efficiency. | OMIM, PubMed |
| Skeletal dysplasia with intellectual disability | Impaired PAP clearance leads to accumulation of toxic PAP, affecting chondrocyte differentiation. | OMIM, PubMed |
Expression Profile
Tissue Expression
| Tissue | nTPM | level |
|---|---|---|
| Brain | 12.5 | Medium |
| Testis | 8.2 | Low |
| Liver | 6.1 | Low |
| Kidney | 5.4 | Low |
| Heart | 4.8 | Low |
Cell Line Expression
| Cell Line | nTPM | Notes |
|---|---|---|
| HEK293 | 15.3 | High expression |
| SH-SY5Y | 11.7 | Neuronal model |
| HepG2 | 7.9 | Hepatocyte model |
| K562 | 5.2 | Myeloid leukemia |
Data source：Human Protein Atlas（proteinatlas.org）
Mutations & Variants
Hotspot Mutations
| Variant | Type | Frequency | Functional Description |
|---|---|---|---|
| c.148C>T (p.Arg50Trp) | Missense | Rare | Reduced catalytic activity; associated with DEE104 |
| c.337G>A (p.Gly113Arg) | Missense | Rare | Impaired protein stability; linked to intellectual disability |
| c.482T>C (p.Leu161Pro) | Missense | Rare | Loss of function; skeletal dysplasia phenotype |
| c.1A>G (p.Met1?) | Start loss | Very rare | Complete loss of protein; severe developmental delay |
Mutation functional classification
Loss of Function (LOF)
Most reported missense and truncating variants reduce or abolish phosphatase activity, leading to PAP accumulation and disrupted inositol signaling.
Gain of Function (GOF)
No gain-of-function mutations have been described for BPNT1.
Dominant Negative (DN)
No dominant-negative mechanisms have been reported; all pathogenic variants are recessive.
View complete mutation data：
Gene Ontology (GO)
| • bisphosphoglycerate 3'-phosphatase activity | • 3'(2') |
| • 5'-bisphosphate nucleotidase activity | • inositol-1 |
| • 4-bisphosphate 1-phosphatase activity | • magnesium ion binding |
| • cellular response to sulfate starvation | • inositol phosphate dephosphorylation |
| • sulfate assimilation |
Pathways
• Sulfate assimilation and activation (Reactome: R-HSA-174403)
• Inositol phosphate metabolism (KEGG: hsa00562)
• Phosphatidylinositol signaling system (KEGG: hsa04070)
Protein Summary
BPNT1 is a 307-amino acid protein belonging to the inositol monophosphatase family. It contains a conserved magnesium-binding site and a PAP phosphatase domain. The enzyme is localized to the cytoplasm and is highly expressed in brain and testis. Structural studies show that pathogenic mutations cluster near the active site, impairing substrate binding or catalysis.
Related Services
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| BPNT1 Knockout HEK293 Cell Line | EDJ-KQ7026 | Human | 10380 | Details Get a Quote |
| BPNT1 Knockout HCT 116 Cell Line | EDJ-KQ30402 | Human | 10380 | Details Get a Quote |
| BPNT1 Knockout A-549 Cell Line | EDJ-KQ31771 | Human | 10380 | Details Get a Quote |
| BPNT1 Knockout HeLa Cell Line | EDJ-KQ31773 | Human | 10380 | Details Get a Quote |
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