INO80D

INO80 complex subunit D, the group of INO80 complex

Basic information

Region (hg38): 2:205993721-206086303

Links

ENSG00000114933 ∙ NCBI:54891 ∙ OMIM:619207 ∙ HGNC:25997 ∙ Uniprot:Q53TQ3 ∙ 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 INO80D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INO80D 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			67	2	2	71
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	67	2	2

Variants in INO80D

This is a list of pathogenic ClinVar variants found in the INO80D region.

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

Position	Type	Phenotype	Significance	ClinVar
2-206004399-T-C		not specified	Uncertain significance (May 15, 2023)
2-206004552-G-A		not specified	Uncertain significance (Feb 09, 2025)
2-206004600-G-C		not specified	Uncertain significance (Sep 28, 2022)
2-206004607-G-A		not specified	Uncertain significance (Sep 20, 2024)
2-206004643-C-T		not specified	Uncertain significance (Apr 10, 2023)
2-206004649-C-T		not specified	Uncertain significance (Jun 03, 2022)
2-206004678-G-A		not specified	Uncertain significance (Sep 05, 2024)
2-206004684-G-A		not specified	Uncertain significance (Sep 15, 2021)
2-206004727-C-T		not specified	Uncertain significance (Jan 10, 2025)
2-206004756-T-C		not specified	Uncertain significance (Feb 27, 2024)
2-206004805-C-T		not specified	Uncertain significance (Jul 16, 2024)
2-206004811-C-T		not specified	Uncertain significance (Sep 27, 2022)
2-206004951-T-C		not specified	Uncertain significance (Jan 26, 2022)
2-206004966-T-C		not specified	Uncertain significance (Jun 22, 2024)
2-206005104-T-C		not specified	Uncertain significance (Mar 05, 2025)
2-206005113-A-G		not specified	Uncertain significance (Feb 21, 2024)
2-206005191-C-A		not specified	Uncertain significance (Dec 12, 2023)
2-206005215-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-206005293-C-T		not specified	Uncertain significance (Feb 12, 2025)
2-206005332-C-T		not specified	Uncertain significance (Aug 30, 2022)
2-206005378-C-A		not specified	Uncertain significance (Mar 08, 2025)
2-206005386-C-T		not specified	Uncertain significance (Dec 20, 2021)
2-206005420-C-G		not specified	Uncertain significance (Jan 10, 2023)
2-206005440-A-G		not specified	Uncertain significance (Jul 11, 2023)
2-206005502-T-G		not specified	Uncertain significance (Dec 09, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INO80D	protein_coding	protein_coding	ENST00000403263	9	92583

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000384	124650	0	9	124659	0.0000361

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.74	390	575	0.678	0.0000317	6699
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000355	0.0000354
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

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.
• Pathway: Gastric Cancer Network 1;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: 0.0853

Intolerance Scores

• loftool: 0.498
• rvis_EVS: -0.46
• rvis_percentile_EVS: 23.63

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.783
• ghis: 0.580

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ino80d

Gene ontology

• Biological process: DNA repair;DNA recombination;protein deubiquitination
• Cellular component: nucleus;nucleoplasm