IPO9
protein-codingimportin 9, the group of MicroRNA protein coding host genes|Importins
Gene summary
Enables histone binding activity; histone chaperone activity; and nuclear import signal receptor activity. Involved in proteasome localization and protein import into nucleus. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~55.1 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 IPO9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018085.5. 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 | 2 | 1 | 3 | |||
| missense | 97 | 1 | 98 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 105 | 1 | 1 | 107 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060555.2 | 24 | MANE Select | |
| Ensembl | ENSP00000354742.4 | 24 | MANE Select | |
| Ensembl | ENSP00000387761.1 | 4 | Standard | |
| Ensembl | ENSP00000556618.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein import into nucleus
Molecular Function
- protein binding
- Ran GTPase binding
- protein transporter activity
- histone binding
Cellular Component
- nuclear envelope
- cytoplasm
- cytosol
- membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361565
- Coding exons
- 24
- Length
- 55154
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 14
- Defined
- 125748
- p
- 0.0000557
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.28 | 356 | 578 | 0.616 | 0.0000308 | 6831 |
| Missense (PolyPhen) | 52 | 147.02 | 0.35369 | 1664 | ||
| Synonymous | 1.00 | 196 | 215 | 0.913 | 0.0000114 | 2038 |
| Loss of Function | 6.15 | 7 | 57.2 | 0.122 | 0.00000291 | 624 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.000044 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00031 | 0.00030 | rare |
| East Asian | 0.000055 | 0.000054 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000055 | 0.000053 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions in nuclear protein import as nuclear transport receptor (PubMed:11823430). Serves as receptor for nuclear localization signals (NLS) in cargo substrates (PubMed:11823430). Is thought to mediate docking of the importin/substrate complex to the nuclear pore complex (NPC) through binding to nucleoporin and the complex is subsequently translocated through the pore by an energy requiring, Ran-dependent mechanism (PubMed:11823430). At the nucleoplasmic side of the NPC, Ran binds to the importin, the importin/substrate complex dissociates and importin is re-exported from the nucleus to the cytoplasm where GTP hydrolysis releases Ran (PubMed:11823430). The directionality of nuclear import is thought to be conferred by an asymmetric distribution of the GTP- and GDP-bound forms of Ran between the cytoplasm and nucleus (PubMed:11823430). Mediates the nuclear import of RPS7, RPL18A, RPL6, histone H2A, histone H2B and histone (PubMed:11823430). Prevents the cytoplasmic aggregation of RPS7 and RPL18A by shielding exposed basic domains (PubMed:11823430). Mediates the nuclear import of actin (By similarity). {ECO:0000250|UniProtKB:Q91YE6, ECO:0000269|PubMed:11823430}.;
Recessive Scores
- pRec
- 0.335
Intolerance Scores
- LoFtool
- 0.252
- RVIS EVS
- -1.29
- RVIS percentile EVS
- 5.03
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.806
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |