INO80
INO80 complex ATPase subunit, the group of INO80 complex |DNA helicases
Basic information
Region (hg38): 15:40978880-41116280
Previous symbols: [ "INOC1" ]
Links
Phenotypes
GenCC
Source:
- immunodeficiency, common variable, 1 (Disputed Evidence), mode of inheritance: AR
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (142 variants)
- not_provided (26 variants)
- INO80-related_disorder (25 variants)
- INO80-related_immunodeficiency (2 variants)
- Primary_microcephaly (2 variants)
- Seizure (2 variants)
- Intellectual_disability (2 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the INO80 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017553.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 14 | 24 | ||||
| missense | 154 | 166 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | |||||
| Total | 0 | 2 | 166 | 22 | 7 |
Highest pathogenic variant AF is 0.00021159384
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| INO80 | protein_coding | protein_coding | ENST00000361937 | 35 | 137475 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 7.14e-14 | 125725 | 0 | 23 | 125748 | 0.0000915 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.53 | 577 | 870 | 0.663 | 0.0000494 | 10221 |
| Missense in Polyphen | 144 | 355.7 | 0.40484 | 4089 | ||
| Synonymous | -0.720 | 331 | 315 | 1.05 | 0.0000165 | 2960 |
| Loss of Function | 8.78 | 3 | 95.7 | 0.0313 | 0.00000590 | 1029 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000188 | 0.000185 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.000326 | 0.000323 |
| European (Non-Finnish) | 0.0000797 | 0.0000791 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: ATPase component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and DNA repair (PubMed:16230350, PubMed:16298340, PubMed:17721549, PubMed:20855601, PubMed:20237820). Binds DNA (PubMed:16298340, PubMed:21303910). As part of the INO80 complex, remodels chromatin by shifting nucleosomes (PubMed:16230350, PubMed:21303910). Regulates transcription upon recruitment by YY1 to YY1-activated genes, where it acts as an essential coactivator (PubMed:17721549). Involved in UV-damage excision DNA repair (PubMed:20855601). The contribution to DNA double-strand break repair appears to be largely indirect through transcriptional regulation (PubMed:20687897). Involved in DNA replication (PubMed:20237820). Required for microtubule assembly during mitosis thereby regulating chromosome segregation cycle (PubMed:20237820). {ECO:0000269|PubMed:16230350, ECO:0000269|PubMed:16298340, ECO:0000269|PubMed:17721549, ECO:0000269|PubMed:20237820, ECO:0000269|PubMed:20687897, ECO:0000269|PubMed:20855601, ECO:0000269|PubMed:21303910}.;
- Pathway
- DNA Repair;Post-translational protein modification;Metabolism of proteins;UCH proteinases;Deubiquitination;DNA Damage Recognition in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair
(Consensus)
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- loftool
- 0.0167
- rvis_EVS
- -1.1
- rvis_percentile_EVS
- 6.93
Haploinsufficiency Scores
- pHI
- 0.643
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.570
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ino80
- Phenotype
- cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; reproductive system phenotype; neoplasm; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype;
Gene ontology
- Biological process
- mitotic sister chromatid segregation;double-strand break repair via homologous recombination;DNA repair;double-strand break repair;chromatin remodeling;transcription, DNA-templated;positive regulation of nuclear cell cycle DNA replication;protein deubiquitination;positive regulation of cell growth;DNA duplex unwinding;cellular response to UV;nucleosome mobilization;ATP-dependent chromatin remodeling;regulation of transcription from RNA polymerase II promoter in response to stress;positive regulation of transcription by RNA polymerase II;spindle assembly;cell division;UV-damage excision repair;cellular response to ionizing radiation;regulation of G1/S transition of mitotic cell cycle
- Cellular component
- nucleus;nucleoplasm;cytoplasm;spindle;microtubule;plasma membrane;nuclear body;Ino80 complex;intermediate filament cytoskeleton
- Molecular function
- DNA binding;actin binding;protein binding;ATP binding;DNA-dependent ATPase activity;ATPase activity;histone binding;alpha-tubulin binding;ATP-dependent 3'-5' DNA helicase activity