IMPA2
protein-codinginositol monophosphatase 2, the group of Phosphoinositide phosphatases
Gene summary
This locus encodes an inositol monophosphatase. The encoded protein catalyzes the dephosphoylration of inositol monophosphate and plays an important role in phosphatidylinositol signaling. This locus may be associated with susceptibility to bipolar disorder. [provided by RefSeq, Jan 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~49.9 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 IMPA2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014214.3. 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 | 49 | 2 | 1 | 52 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 54 | 2 | 1 | 57 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055029.1 | 8 | MANE Select | |
| Ensembl | ENSP00000269159.3 | 8 | MANE Select | |
| Ensembl | ENSP00000372867.4 | 3 | Standard | |
| Ensembl | ENSP00000464754.1 | 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)
- superpathway of D-<i>myo</i>-inositol (1,4,5)-trisphosphate metabolism
- Inositol phosphate metabolism
- D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation
Biological Process
- inositol biosynthetic process
- phosphate-containing compound metabolic process
- signal transduction
- inositol phosphate metabolic process
- phosphatidylinositol phosphorylation
Molecular Function
- protein binding
- inositol monophosphate 1-phosphatase activity
- protein homodimerization activity
- metal ion binding
- inositol monophosphate 3-phosphatase activity
Cellular Component
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000269159
- Coding exons
- 8
- Length
- 49853
- Individuals with no LoFs
- 125730
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125748
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.851 | 140 | 171 | 0.817 | 0.0000114 | 1827 |
| Missense (PolyPhen) | 52 | 75.585 | 0.68797 | 780 | ||
| Synonymous | 0.695 | 64 | 71.5 | 0.895 | 0.00000499 | 614 |
| Loss of Function | 1.77 | 7 | 14.2 | 0.492 | 8.38e-7 | 170 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00015 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000070 | 0.000070 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Can use myo-inositol monophosphates, scylloinositol 1,4- diphosphate, glucose-1-phosphate, beta-glycerophosphate, and 2'- AMP as substrates. Has been implicated as the pharmacological target for lithium Li(+) action in brain. {ECO:0000269|PubMed:17068342}.;
Recessive Scores
- pRec
- 0.236
Intolerance Scores
- LoFtool
- 0.424
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.898
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |