INO80

INO80 complex ATPase subunit, the group of INO80 complex |DNA helicases

Basic information

Region (hg38): 15:40978880-41116280

Previous symbols: [ "INOC1" ]

Links

ENSG00000128908 ∙ NCBI:54617 ∙ OMIM:610169 ∙ HGNC:26956 ∙ Uniprot:Q9ULG1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• immunodeficiency, common variable, 1 (Disputed Evidence), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INO80 gene.

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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	13	4	18
missense			61	6	2	69
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding				1	7	8
Total	0	0	63	20	13

Variants in INO80

This is a list of pathogenic ClinVar variants found in the INO80 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-40980290-C-A		not specified	Uncertain significance (Nov 15, 2021)
15-40980293-G-A		INO80-related disorder	Likely benign (Mar 21, 2022)
15-40980317-C-T		not specified	Uncertain significance (Mar 24, 2023)
15-40980340-C-G		not specified	Uncertain significance (Nov 09, 2021)
15-40980363-A-T		not specified	Uncertain significance (May 09, 2022)
15-40980393-C-T		not specified	Uncertain significance (May 31, 2023)
15-40980399-G-C		not specified	Uncertain significance (Sep 27, 2021)
15-40980401-C-T		not specified	Uncertain significance (Jan 17, 2023)
15-40982816-T-G		not specified	Benign (Jan 24, 2024)
15-40982886-C-T		INO80-related disorder	Uncertain significance (Apr 28, 2023)
15-40982932-T-C		INO80-related disorder	Likely benign (Feb 20, 2019)
15-40982972-C-T		not specified	Uncertain significance (Jun 07, 2023)
15-40983021-C-G		not specified	Uncertain significance (Dec 16, 2022)
15-40983024-G-A		INO80-related disorder	Uncertain significance (Aug 11, 2023)
15-40983037-G-C		not specified	Uncertain significance (Jan 31, 2024)
15-40983060-T-C			Uncertain significance (Apr 23, 2018)
15-40983780-C-T		not specified	Uncertain significance (Apr 16, 2024)
15-40983781-G-A		INO80-related disorder	Likely benign (Jun 08, 2023)
15-40983837-C-G			Uncertain significance (May 27, 2022)
15-40983960-G-A		not specified	Benign (Jan 24, 2024)
15-40984217-T-C		not specified	Uncertain significance (Apr 08, 2024)
15-40984256-C-G		See cases • INO80-related disorder	Uncertain significance (Jun 23, 2023)
15-40984264-T-C		not specified	Uncertain significance (Nov 08, 2022)
15-40984279-G-A		INO80-related disorder	Likely benign (Aug 14, 2024)
15-40984294-A-G		not specified	Uncertain significance (May 06, 2022)

GnomAD

Source: gnomAD

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: dbNSFP

• 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