INO80C

INO80 complex subunit C, the group of INO80 complex

Basic information

Region (hg38): 18:35452230-35497979

Previous symbols: [ "C18orf37" ]

Links

ENSG00000153391 ∙ NCBI:125476 ∙ ∙ HGNC:26994 ∙ Uniprot:Q6PI98 ∙ 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 INO80C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INO80C 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	1
missense			25	1		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	25	1	1

Variants in INO80C

This is a list of pathogenic ClinVar variants found in the INO80C region.

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

Position	Type	Phenotype	Significance	ClinVar
18-35468622-T-C		not specified	Uncertain significance (Oct 05, 2023)
18-35468653-G-A			Benign (Dec 31, 2019)
18-35468658-C-T		not specified	Uncertain significance (Jan 26, 2022)
18-35468660-A-G		not specified	Uncertain significance (Oct 24, 2024)
18-35468682-T-A		not specified	Uncertain significance (Apr 19, 2024)
18-35468712-G-A		not specified	Uncertain significance (May 18, 2022)
18-35478331-G-A		not specified	Uncertain significance (Jul 19, 2023)
18-35478355-A-G			Benign (Dec 31, 2019)
18-35479342-C-T		not specified	Uncertain significance (Feb 07, 2025)
18-35479393-C-T		not specified	Uncertain significance (Jul 26, 2024)
18-35480454-A-C		not specified	Uncertain significance (Nov 21, 2024)
18-35480503-G-A		not specified	Uncertain significance (Dec 06, 2021)
18-35480527-C-A		not specified	Uncertain significance (Dec 01, 2022)
18-35480562-C-T		not specified	Uncertain significance (Jul 07, 2024)
18-35480563-C-T		not specified	Uncertain significance (May 13, 2024)
18-35497729-C-T		not specified	Uncertain significance (Dec 06, 2022)
18-35497733-A-C		not specified	Uncertain significance (Sep 16, 2021)
18-35497733-A-G		not specified	Uncertain significance (Dec 14, 2023)
18-35497739-A-C		not specified	Uncertain significance (Mar 25, 2024)
18-35497763-C-T		not specified	Likely benign (Sep 25, 2024)
18-35497765-T-A		not specified	Uncertain significance (Sep 09, 2024)
18-35497765-T-G		not specified	Uncertain significance (Apr 15, 2022)
18-35497766-A-G		not specified	Uncertain significance (Sep 09, 2024)
18-35497799-T-A		not specified	Uncertain significance (Nov 21, 2023)
18-35497807-C-T		not specified	Uncertain significance (Jun 29, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INO80C	protein_coding	protein_coding	ENST00000441607	7	45762

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000415	0.659	125725	0	23	125748	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.104	122	119	1.03	0.00000634	1468
Missense in Polyphen		28	34.352	0.81508		420
Synonymous	-0.133	50	48.8	1.02	0.00000293	452
Loss of Function	0.740	6	8.30	0.723	3.49e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000109	0.000105
Middle Eastern	0.000164	0.000163
South Asian	0.0000981	0.0000980
Other	0.000496	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Proposed core component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.
• 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: 0.0871

Intolerance Scores

• loftool: 0.318
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.154
• hipred: N
• hipred_score: 0.458
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ino80c

Gene ontology

• Biological process: DNA repair;DNA recombination;chromatin remodeling;biological_process;protein deubiquitination
• Cellular component: fibrillar center;nucleoplasm;Ino80 complex;MLL1 complex
• Molecular function: molecular_function