INPP1
protein-codinginositol polyphosphate-1-phosphatase, the group of Phosphoinositide phosphatases
Gene summary
This gene encodes the enzyme inositol polyphosphate-1-phosphatase, one of the enzymes involved in phosphatidylinositol signaling pathways. This enzyme removes the phosphate group at position 1 of the inositol ring from the polyphosphates inositol 1,4-bisphosphate and inositol 1,3,4-trisphophosphate. [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 ~28.1 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 INPP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001128928.2. 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 | 52 | 5 | 57 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 57 | 5 | 1 | 63 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001122400.1 | 5 | MANE Select | |
| Ensembl | ENSP00000376142.2 | 5 | MANE Select | |
| RefSeq | NP_002185.1 | 5 | Standard | |
| Ensembl | ENSP00000325423.4 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Inositol phosphate metabolism - Homo sapiens (human)
- Phosphatidylinositol signaling system - Homo sapiens (human)
- Inositol Phosphate Metabolism
- Inositol Metabolism
- superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism
Biological Process
- phosphate-containing compound metabolic process
- signal transduction
- inositol phosphate metabolic process
- phosphatidylinositol phosphorylation
- inositol phosphate dephosphorylation
Molecular Function
- inositol-1,4-bisphosphate 1-phosphatase activity
- protein binding
- metal ion binding
- inositol-1,3,4-trisphosphate 1-phosphatase activity
Cellular Component
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000392329
- Coding exons
- 5
- Length
- 28196
- Individuals with no LoFs
- 125547
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 199
- Defined
- 125747
- p
- 0.000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 168 | 217 | 0.774 | 0.0000108 | 2600 |
| Missense (PolyPhen) | 60 | 87.279 | 0.68745 | 1120 | ||
| Synonymous | 0.728 | 73 | 81.3 | 0.897 | 0.00000408 | 795 |
| Loss of Function | 0.808 | 11 | 14.3 | 0.769 | 6.97e-7 | 180 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00037 | 0.00037 | rare |
| Latino/Admixed American | 0.00032 | 0.00029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.0012 | 0.0012 | notable |
| South Asian | 0.00082 | 0.00082 | rare |
| Other | 0.0012 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- LoFtool
- 0.714
- RVIS EVS
- 0.13
- RVIS percentile EVS
- 63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.929
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |