INO80D

protein-coding

INO80 complex subunit D, 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. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_017759.5

Inheritance

—

ClinVar variants

U:123B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.1

Max pathogenic AF

—

Genomic locus

chr2:205,993,721-206,086,303

External References & Databases

Ensembl (ENSG00000114933)

Transcript & Mutation Effects

hg38 • Region Span ~92.6 kb

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GenCC 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 INO80D variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 117

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017759.5. 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 clinvar			2
missense			119 clinvar	2 clinvar	2 clinvar	123
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	123	2	2	127

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017759.5	RefSeq	NP_060229.3	9	MANE Select
ENST00000403263.6	Ensembl	ENSP00000384198.1	9	MANE Select
ENST00000414320.1	Ensembl	ENSP00000409031.1	1	Standard
ENST00000424117.5	Ensembl	ENSP00000402369.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gastric Cancer Network 1
DNA Repair
Post-translational protein modification
Metabolism of proteins
UCH proteinases

Biological Process

DNA repair
DNA recombination
protein deubiquitination

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000403263
Coding exons: 9
Length: 92583
Individuals with no LoFs: 124650
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 124659
p: 0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.74	390	575	0.678	0.0000317	6699
Missense (PolyPhen)		109	207.26	0.52592		2514
Synonymous	0.119	225	227	0.990	0.0000128	2095
Loss of Function	5.29	4	40.2	0.0995	0.00000238	451

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.000035	0.000035	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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: 0.0853

Intolerance Scores

LoFtool: 0.498
RVIS EVS: -0.46
RVIS percentile EVS: 23.63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): K
Indispensability pred.: E
Indispensability score: 0.768

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	High
Cancer	Medium	Medium	Medium