INO80B

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

Basic information

Region (hg38): 2:74455086-74457944

Previous symbols: [ "HMGA1L4", "ZNHIT4" ]

Links

ENSG00000115274 ∙ NCBI:83444 ∙ OMIM:616456 ∙ HGNC:13324 ∙ Uniprot:Q9C086 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the INO80B gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INO80B 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						0
missense			18			18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	0	0

Variants in INO80B

This is a list of pathogenic ClinVar variants found in the INO80B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74455138-G-A		not specified	Uncertain significance (Feb 10, 2022)
2-74455430-C-T		not specified	Uncertain significance (Jan 03, 2024)
2-74455433-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-74455519-G-A		not specified	Uncertain significance (Feb 16, 2023)
2-74455546-C-T		not specified	Uncertain significance (Oct 05, 2023)
2-74456244-T-C		not specified	Uncertain significance (May 26, 2022)
2-74456249-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-74457352-G-T		not specified	Uncertain significance (Jan 07, 2022)
2-74457356-G-A		not specified	Uncertain significance (Apr 19, 2023)
2-74457364-C-T		not specified	Uncertain significance (Dec 16, 2021)
2-74457370-C-T		not specified	Uncertain significance (Jan 12, 2024)
2-74457529-G-A		not specified	Uncertain significance (Apr 26, 2023)
2-74457563-C-T		not specified	Uncertain significance (Apr 07, 2023)
2-74457595-G-A		not specified	Uncertain significance (Apr 28, 2022)
2-74457607-A-T		not specified	Uncertain significance (Dec 07, 2021)
2-74457616-T-C		not specified	Uncertain significance (Feb 15, 2023)
2-74457695-C-G		not specified	Uncertain significance (Jun 02, 2023)
2-74457700-T-A		not specified	Uncertain significance (Aug 01, 2022)
2-74457706-C-G		not specified	Uncertain significance (May 18, 2022)
2-74457709-C-T		not specified	Uncertain significance (Apr 17, 2023)
2-74457712-C-T		not specified	Uncertain significance (Feb 14, 2023)
2-74457746-G-T		not specified	Uncertain significance (Aug 01, 2022)
2-74457854-T-G		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INO80B	protein_coding	protein_coding	ENST00000233331	5	5862

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.759	0.241	125729	0	19	125748	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.731	164	193	0.852	0.00000933	2216
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000509	0.000495
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces growth and cell cycle arrests at the G1 phase of the cell cycle. {ECO:0000269|PubMed:15556297}.
• 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: 0.106

Intolerance Scores

• loftool: 0.488
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.831
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ino80b
• Phenotype: embryo phenotype

Gene ontology

• Biological process: DNA repair;DNA recombination;chromatin remodeling;protein deubiquitination
• Cellular component: nucleus;nucleoplasm;nucleolus;Ino80 complex
• Molecular function: protein binding;metal ion binding