INO80E
protein-codingINO80 complex subunit E, the group of INO80 complex
Gene summary
Involved in several processes, including positive regulation of DNA-templated transcription; regulation of DNA metabolic process; and regulation of chromosome organization. Located in nucleolus and nucleoplasm. Part of Ino80 complex. [provided by Alliance of Genome Resources, Jun 2026]
- CCDC95
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.1 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 INO80E variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173618.3. 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 | 2 | |||
| missense | 55 | 1 | 56 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 57 | 2 | 0 | 59 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_775889.1 | 7 | MANE Select | |
| Ensembl | ENSP00000457016.1 | 7 | MANE Select | |
| RefSeq | NP_001291491.1 | 6 | Standard | |
| RefSeq | NP_001291492.1 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ino80e | Danio rerio | Structure: pigment cell Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- DNA Repair
- Post-translational protein modification
- Metabolism of proteins
- UCH proteinases
- Deubiquitination
Biological Process
- DNA repair
- DNA recombination
- chromatin remodeling
- protein deubiquitination
Molecular Function
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- nucleolus
- Ino80 complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000563197
- Coding exons
- 7
- Length
- 10500
- Individuals with no LoFs
- 125689
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 49
- Defined
- 125738
- p
- 0.000195
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.254 | 138 | 130 | 1.06 | 0.00000763 | 1507 |
| Missense (PolyPhen) | 78 | 75.879 | 1.0279 | 908 | ||
| Synonymous | -1.07 | 71 | 60.4 | 1.18 | 0.00000370 | 522 |
| Loss of Function | 1.69 | 5 | 11.1 | 0.452 | 4.81e-7 | 137 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000066 | 0.000062 | rare |
| Latino/Admixed American | 0.000063 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.000057 | 0.000054 | rare |
| Finnish | 0.000055 | 0.000046 | rare |
| European (Non-Finnish) | 0.00043 | 0.00033 | rare |
| South Asian | 0.00014 | 0.00013 | rare |
| Other | 0.00019 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.;
Recessive Scores
- pRec
- 0.110
Intolerance Scores
- LoFtool
- 0.344
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.12
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.577
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |