INO80B

protein-coding

INO80 complex subunit B, the group of Zinc fingers HIT-type|INO80 complex

Gene summary

This gene encodes a subunit of an ATP-dependent chromatin remodeling complex, INO80, which plays a role in DNA and nucleosome-activated ATPase activity and ATP-dependent nucleosome sliding. Readthrough transcription of this gene into the neighboring downstream gene, which encodes WW domain-binding protein 1, generates a non-coding transcript. [provided by RefSeq, Feb 2011]

Previous symbols:

HMGA1L4
ZNHIT4

MANE transcript

NM_031288.4

Inheritance

—

ClinVar variants

U:47B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr2:74,455,087-74,457,944

External References & Databases

Ensembl (ENSG00000115274)

Transcript & Mutation Effects

hg38 • Region Span ~2.9 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 INO80B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031288.4. 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 clinvar		1
missense			47 clinvar	1 clinvar		48
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	47	2	0	49

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031288.4	RefSeq	NP_112578.2	5	MANE Select
ENST00000233331.12	Ensembl	ENSP00000233331.7	5	MANE Select
ENST00000409493.3	Ensembl	ENSP00000386937.2	5	Standard
ENST00000409917.5	Ensembl	ENSP00000387267.1	5	Standard

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
metal ion binding

Cellular Component

nucleus
nucleoplasm
nucleolus
Ino80 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000233331
Coding exons: 5
Length: 5862
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125748
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.731	164	193	0.852	0.00000933	2216
Missense (PolyPhen)		51	89.209	0.57169		1110
Synonymous	-1.76	101	80.8	1.25	0.00000358	783
Loss of Function	2.89	2	13.4	0.149	6.36e-7	159

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000075	0.000062	rare
Latino/Admixed American	0.00043	0.00043	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Induces growth and cell cycle arrests at the G1 phase of the cell cycle. {ECO:0000269|PubMed:15556297}.;

Recessive Scores

pRec: 0.106

Intolerance Scores

LoFtool: 0.488
RVIS EVS: -0.21
RVIS percentile EVS: 38.28

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.968

Gene Damage Prediction

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