BPNT1
protein-coding3'(2'), 5'-bisphosphate nucleotidase 1, the group of Phosphoinositide phosphatases
Gene summary
BPNT1, also called bisphosphate 3-prime-nucleotidase, or BPntase, is a member of a magnesium-dependent phosphomonoesterase family. Lithium, a major drug used to treat manic depression, acts as an uncompetitive inhibitor of BPntase. The predicted human protein is 92% identical to mouse BPntase. BPntase's physiologic role in nucleotide metabolism may be regulated by inositol signaling pathways. The inhibition of human BPntase may account for lithium-induced nephrotoxicity. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~33.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BPNT1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006085.6. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 1 | 31 | 1 | 33 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 1 | 0 | 35 | 1 | 0 | 37 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006076.4 | 8 | MANE Select | |
| Ensembl | ENSP00000318852.7 | 8 | MANE Select | |
| RefSeq | NP_001273078.1 | 7 | Standard | |
| RefSeq | NP_001273079.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Sulfur metabolism - Homo sapiens (human)
- Sulfate/Sulfite Metabolism
- Sulfite oxidase deficiency
- Phase II - Conjugation of compounds
- Biological oxidations
Biological Process
- nucleobase-containing compound metabolic process
- nervous system development
- dephosphorylation
- phosphatidylinositol phosphorylation
- 3'-phosphoadenosine 5'-phosphosulfate metabolic process
Molecular Function
- 3'(2'),5'-bisphosphate nucleotidase activity
- metal ion binding
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000469520
- Coding exons
- 8
- Length
- 32981
- Individuals with no LoFs
- 124772
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 22
- Defined
- 124794
- p
- 0.0000881
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.36 | 119 | 169 | 0.706 | 0.00000850 | 1982 |
| Missense (PolyPhen) | 49 | 71.106 | 0.68911 | 822 | ||
| Synonymous | 0.389 | 56 | 59.8 | 0.936 | 0.00000292 | 617 |
| Loss of Function | 1.62 | 10 | 17.2 | 0.580 | 9.65e-7 | 198 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.000061 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000056 | 0.000056 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000089 | 0.000088 | rare |
| South Asian | 0.00020 | 0.00020 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Converts adenosine 3'-phosphate 5'-phosphosulfate (PAPS) to adenosine 5'-phosphosulfate (APS) and 3'(2')-phosphoadenosine 5'- phosphate (PAP) to AMP. Has 1000-fold lower activity towards inositol 1,4-bisphosphate (Ins(1,4)P2) and inositol 1,3,4- trisphosphate (Ins(1,3,4)P3), but does not hydrolyze Ins(1)P, Ins(3,4)P2, Ins(1,3,4,5)P4 or InsP6. {ECO:0000269|PubMed:10224133}.;
Recessive Scores
- pRec
- 0.0964
Intolerance Scores
- LoFtool
- 0.657
- RVIS EVS
- 0.46
- RVIS percentile EVS
- 78.28
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |