INO80E

INO80 complex subunit E, the group of INO80 complex

Basic information

Region (hg38): 16:29995714-30005793

Previous symbols: [ "CCDC95" ]

Links

ENSG00000169592 ∙ NCBI:283899 ∙ ∙ HGNC:26905 ∙ Uniprot:Q8NBZ0 ∙ 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 INO80E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INO80E 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in INO80E

This is a list of pathogenic ClinVar variants found in the INO80E region.

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

Position	Type	Phenotype	Significance	ClinVar
16-29996602-T-G		not specified	Uncertain significance (Dec 27, 2023)
16-29996818-G-C		not specified	Uncertain significance (Nov 21, 2022)
16-29996836-G-C		not specified	Uncertain significance (Aug 17, 2022)
16-29996851-G-A		not specified	Uncertain significance (Oct 12, 2021)
16-30000793-A-G		not specified	Uncertain significance (Oct 30, 2023)
16-30000794-C-T		not specified	Uncertain significance (Aug 12, 2021)
16-30000803-C-T		not specified	Uncertain significance (Feb 21, 2024)
16-30000824-C-T		not specified	Uncertain significance (Jan 12, 2024)
16-30000832-A-G		not specified	Uncertain significance (Mar 16, 2022)
16-30000953-C-T			Likely benign (May 01, 2022)
16-30000954-G-T		not specified	Uncertain significance (Sep 17, 2021)
16-30000955-C-A		not specified	Uncertain significance (Jun 07, 2024)
16-30000955-C-T		not specified	Uncertain significance (Apr 25, 2022)
16-30001020-C-G		not specified	Uncertain significance (Apr 27, 2022)
16-30001027-C-G		not specified	Uncertain significance (Jan 17, 2023)
16-30001421-C-T		not specified	Uncertain significance (May 18, 2023)
16-30001426-C-T		not specified	Uncertain significance (May 11, 2022)
16-30001442-C-T		not specified	Uncertain significance (Nov 13, 2023)
16-30001490-C-A		not specified	Uncertain significance (Feb 10, 2022)
16-30001505-G-A		not specified	Uncertain significance (Jun 29, 2022)
16-30005231-G-A		not specified	Uncertain significance (Jun 07, 2024)
16-30005296-G-A		not specified	Uncertain significance (Jan 03, 2024)
16-30005308-A-G		not specified	Likely benign (May 04, 2023)
16-30005333-C-T		not specified	Uncertain significance (Oct 26, 2022)
16-30005335-C-G		not specified	Uncertain significance (Jan 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INO80E	protein_coding	protein_coding	ENST00000563197	7	10500

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00868	0.941	125689	0	49	125738	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.254	138	130	1.06	0.00000763	1507
Missense in Polyphen		78	75.879	1.0279		908
Synonymous	-1.07	71	60.4	1.18	0.00000370	522
Loss of Function	1.69	5	11.1	0.452	4.81e-7	137

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000124
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000572	0.0000544
Finnish	0.0000547	0.0000462
European (Non-Finnish)	0.000427	0.000334
Middle Eastern	0.0000572	0.0000544
South Asian	0.000137	0.000131
Other	0.000191	0.000163

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: 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: 0.110

Intolerance Scores

• loftool: 0.344
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• pHI: 0.188
• hipred: Y
• hipred_score: 0.742
• ghis: 0.603

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.577

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ino80e
• Phenotype: growth/size/body region phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: ino80e
• Affected structure: pigment cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

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