INO80D

gene
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Also known as FLJ20309

Summary

INO80D (INO80 complex subunit D, HGNC:25997) is a protein-coding gene on chromosome 2q33.3, encoding INO80 complex subunit D (Q53TQ3). Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Involved in several processes, including chromatin remodeling; regulation of chromosome organization; and regulation of nucleobase-containing compound metabolic process. Part of Ino80 complex.

Source: NCBI Gene 54891 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 135 total
  • MANE Select transcript: NM_017759

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25997
Approved symbolINO80D
NameINO80 complex subunit D
Location2q33.3
Locus typegene with protein product
StatusApproved
AliasesFLJ20309
Ensembl geneENSG00000114933
Ensembl biotypeprotein_coding
OMIM619207
Entrez54891

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 6 protein_coding

ENST00000403263, ENST00000414320, ENST00000424117, ENST00000855655, ENST00000855656, ENST00000855657

RefSeq mRNA: 1 — MANE Select: NM_017759 NM_017759

CCDS: CCDS46500

Canonical transcript exons

ENST00000403263 — 11 exons

ExonStartEnd
ENSE00000784941206019736206019845
ENSE00000784942206028111206028335
ENSE00000784944206046504206046612
ENSE00001129652206007284206007441
ENSE00001129658206009577206009794
ENSE00001172222206017680206017813
ENSE00001234836206063151206063244
ENSE00001234843206085901206086174
ENSE00001557750205993721206005533
ENSE00001621693206062799206063045
ENSE00003578946206056198206056943

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 85.74.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.4572 / max 60.8505, expressed in 1676 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
333464.21891366
333431.2709836
333471.0434586
333440.5478313
333450.3551168
333400.01204
333390.00902

Top tissues by expression

134 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
bone marrow cellCL:000209285.74gold quality
bone marrowUBERON:000237185.25gold quality
sural nerveUBERON:001548885.04gold quality
calcaneal tendonUBERON:000370182.53gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047382.35gold quality
colonic epitheliumUBERON:000039781.15gold quality
corpus callosumUBERON:000233680.74gold quality
skeletal muscle tissueUBERON:000113479.82gold quality
tonsilUBERON:000237279.51gold quality
endometriumUBERON:000129577.01gold quality
gastrocnemiusUBERON:000138876.75gold quality
muscle tissueUBERON:000238576.58gold quality
adrenal tissueUBERON:001830376.56gold quality
muscle of legUBERON:000138376.34gold quality
leukocyteCL:000073876.27gold quality
monocyteCL:000057676.25gold quality
skin of abdomenUBERON:000141676.03gold quality
zone of skinUBERON:000001475.93gold quality
skin of legUBERON:000151175.65gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099175.41gold quality
uterine cervixUBERON:000000275.09gold quality
mucosa of stomachUBERON:000119975.09gold quality
tibial nerveUBERON:000132374.94gold quality
cortical plateUBERON:000534374.93gold quality
ovaryUBERON:000099274.76gold quality
lower esophagus mucosaUBERON:003583474.70gold quality
subcutaneous adipose tissueUBERON:000219074.64gold quality
left ovaryUBERON:000211974.53gold quality
thoracic mammary glandUBERON:000520074.49gold quality
thyroid glandUBERON:000204674.48gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-CURD-10no225.32
E-ANND-3no2.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

742 targeting INO80D, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692A100.0074.406850
HSA-MIR-3613-3P100.0076.367965
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4262100.0073.263931
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-8485100.0077.574731
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-3163100.0077.238605
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-340-5P100.0072.504437
HSA-MIR-3646100.0073.565283
HSA-MIR-4692100.0067.322066
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6758-5P100.0066.211470
HSA-MIR-4768-5P100.0069.492861

Literature-anchored findings (GeneRIF, showing 2)

  • INO80D is a subunit of the human INO80 chromatin remodeling complex; its Ser818Cys mutation has a role in accelerated arterial aging (PMID:25122053)
  • expression levels of CR933609 and INO80D were decreased in CR933609-knockdown NSCLC cells, but only expression levels of INO80D decreased in INO80D knockdown cells. It was shown that there are independent promoters in CR933609 and INO80D (PMID:29750421)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioino80daENSDARG00000104727
mus_musculusIno80dENSMUSG00000040865
rattus_norvegicusIno80dENSRNOG00000024272
drosophila_melanogasterl(3)L1231FBGN0086686
caenorhabditis_elegansWBGENE00016409

Protein

Protein identifiers

INO80 complex subunit DQ53TQ3 (reviewed: Q53TQ3)

All UniProt accessions (3): Q53TQ3, C9JLV2, C9JLZ4

UniProt curated annotations — full annotation on UniProt →

Function. Putative regulatory component of the chromatin remodeling INO80 complex which is involved in transcriptional regulation, DNA replication and probably DNA repair.

Subunit / interactions. Component of the chromatin remodeling INO80 complex; specifically part of a complex module associated with the N-terminus of INO80.

Subcellular location. Nucleus.

Similarity. Belongs to the INO80D family.

RefSeq proteins (1): NP_060229* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR025927Znf_KANL2-likeDomain

Pfam: PF13891

UniProt features (19 total): compositionally biased region 6, region of interest 5, sequence conflict 4, chain 1, modified residue 1, cross-link 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q53TQ3-F152.250.06

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 132, 87

Function

Pathways and Gene Ontology

Reactome pathways

8 pathways

IDPathway
R-HSA-5689603UCH proteinases
R-HSA-5696394DNA Damage Recognition in GG-NER
R-HSA-392499Metabolism of proteins
R-HSA-5688426Deubiquitination
R-HSA-5696398Nucleotide Excision Repair
R-HSA-5696399Global Genome Nucleotide Excision Repair (GG-NER)
R-HSA-597592Post-translational protein modification
R-HSA-73894DNA Repair

MSigDB gene sets: 416 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_CHROMOSOME_ORGANIZATION, RRAGTTGT_UNKNOWN, ATACCTC_MIR202, GOBP_TELOMERE_ORGANIZATION, AP2_Q3, GOBP_POSITIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, CACCAGC_MIR138, GGGTGGRR_PAX4_03, GOBP_REGULATION_OF_DNA_REPAIR, GOBP_REGULATION_OF_TELOMERE_MAINTENANCE, NFKB_C, YY1_02

GO Biological Process (14): telomere maintenance (GO:0000723), regulation of DNA replication (GO:0006275), DNA repair (GO:0006281), regulation of DNA repair (GO:0006282), DNA recombination (GO:0006310), chromatin remodeling (GO:0006338), regulation of chromosome organization (GO:0033044), positive regulation of DNA repair (GO:0045739), positive regulation of DNA-templated transcription (GO:0045893), regulation of embryonic development (GO:0045995), regulation of cell cycle (GO:0051726), regulation of DNA strand elongation (GO:0060382), positive regulation of telomere maintenance in response to DNA damage (GO:1904507), DNA damage response (GO:0006974)

GO Molecular Function (0):

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), Ino80 complex (GO:0031011)

Reactome top-level categories

Rollup of top-6 pathways:

CategoryPathways
Deubiquitination1
Global Genome Nucleotide Excision Repair (GG-NER)1
Post-translational protein modification1
DNA Repair1
Nucleotide Excision Repair1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA metabolic process3
regulation of DNA metabolic process3
DNA repair2
positive regulation of response to stimulus2
telomere organization1
DNA replication1
DNA damage response1
regulation of cellular response to stress1
chromatin organization1
regulation of organelle organization1
chromosome organization1
regulation of DNA repair1
positive regulation of DNA metabolic process1
DNA-templated transcription1
regulation of DNA-templated transcription1
positive regulation of RNA biosynthetic process1
embryo development1
regulation of multicellular organismal development1
cell cycle1
regulation of cellular process1
DNA strand elongation1
positive regulation of telomere maintenance1
telomere maintenance in response to DNA damage1
regulation of telomere maintenance in response to DNA damage1
cellular response to stress1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
nuclear chromosome1
INO80-type complex1

Protein interactions and networks

STRING

1260 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
INO80DINO80EQ8NBZ0754
INO80DMRTO4Q9UKD2498
INO80DNOC3LQ8WTT2486
INO80DINO80BQ9C086455
INO80DMPRIPQ6WCQ1450
INO80DGIN1Q9NXP7449
INO80DK7ENP7K7ENP7442
INO80DINO80CQ6PI98441
INO80DLPIN3Q9BQK8438
INO80DFAM110BQ8TC76433
INO80DTMEM216Q9P0N5425
INO80DMAP3K3Q99759425
INO80DBPIFB1Q8TDL5417
INO80DBUD31P41223411
INO80DATRNO75882406

IntAct

29 interactions, top by confidence:

ABTypeScore
UCHL5PSMD11psi-mi:“MI:0914”(association)0.840
YY1ACTL6Apsi-mi:“MI:0914”(association)0.830
INO80ETFPTpsi-mi:“MI:0914”(association)0.790
YY1TFPTpsi-mi:“MI:0914”(association)0.740
INO80CYY1psi-mi:“MI:0914”(association)0.740
RUVBL2POLR3Apsi-mi:“MI:0914”(association)0.640
RUVBL1POLR3Apsi-mi:“MI:0914”(association)0.640
INO80EACTL6Apsi-mi:“MI:0914”(association)0.640
YY1YY2psi-mi:“MI:0914”(association)0.570
Ruvbl1AAR2psi-mi:“MI:0914”(association)0.350
Ruvbl2TTI2psi-mi:“MI:0914”(association)0.350
ACTR5TBRG1psi-mi:“MI:0914”(association)0.350
ESR1ESYT2psi-mi:“MI:0914”(association)0.350
UCHL5PSMD11psi-mi:“MI:0914”(association)0.350
INO80ACTL6Bpsi-mi:“MI:0914”(association)0.350
TFPTCCP110psi-mi:“MI:0914”(association)0.350
INO80ECHD1psi-mi:“MI:0914”(association)0.350
INO80BACTL6Apsi-mi:“MI:0914”(association)0.350
ACTR8ACTL6Apsi-mi:“MI:0914”(association)0.350
ACTL6ATFPTpsi-mi:“MI:0914”(association)0.350
MCRS1ACTL6Apsi-mi:“MI:0914”(association)0.350
INO80DACTL6Apsi-mi:“MI:0914”(association)0.350

BioGRID (64): INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), MED15 (Negative Genetic), INO80D (Positive Genetic), INO80D (Affinity Capture-RNA), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Affinity Capture-MS), INO80D (Positive Genetic)

ESM2 similar proteins: A0A0R4IBL7, A2A891, A3RK74, A4L7N3, B5DE09, E1BPQ1, G3V7R4, O15014, O43524, P11420, P15806, P15881, P15884, P15923, P21677, P30985, P51514, P70365, P98180, Q01978, Q12778, Q14135, Q15596, Q15788, Q4PJW2, Q53TQ3, Q60420, Q60722, Q61026, Q61286, Q62655, Q66IY8, Q66JJ0, Q6DIH5, Q6EUW2, Q6NZT6, Q6PCG7, Q7T2G1, Q7ZXS3, Q80V24

Diamond homologs: A1L1F6, Q2NL14, Q53TQ3, Q54J07, Q566I1, Q5R802, Q66JY2, Q6AY70, Q861R7, Q8BQR4, Q9H9L4

SIGNOR signaling

1 interactions.

AEffectBMechanism
INO80D“form complex”“INO80 complex”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 26 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Global Genome Nucleotide Excision Repair (GG-NER)10228.4×3e-21
DNA Damage Recognition in GG-NER11157.0×3e-21
Nucleotide Excision Repair10142.8×6e-19
UCH proteinases1380.7×3e-21
Deubiquitination1062.1×4e-15
DNA Repair1049.2×3e-14
Chromatin organization520.4×6e-05
Chromatin modifying enzymes518.1×9e-05

GO biological processes:

GO termPartnersFoldFDR
positive regulation of telomere maintenance in response to DNA damage13608.5×3e-35
regulation of DNA strand elongation13570.5×7e-35
regulation of chromosome organization13507.1×7e-34
regulation of DNA replication13198.4×6e-27
positive regulation of DNA repair13194.2×7e-27
regulation of embryonic development13179.0×2e-26
DNA recombination11154.5×2e-21
regulation of DNA repair13149.6×2e-25

Disease & clinical

Clinical variants and AI predictions

ClinVar

135 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance118
Likely benign2
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

2731 predictions. Top by Δscore:

VariantEffectΔscore
2:206007278:CTATA:Cdonor_loss1.0000
2:206007279:TATA:Tdonor_loss1.0000
2:206007280:ATACC:Adonor_loss1.0000
2:206007281:TAC:Tdonor_loss1.0000
2:206007283:C:CAdonor_loss1.0000
2:206007346:T:TAdonor_gain1.0000
2:206007439:CTC:Cacceptor_gain1.0000
2:206007441:CCTGG:Cacceptor_loss1.0000
2:206007442:C:CCacceptor_gain1.0000
2:206019698:A:ACdonor_gain1.0000
2:206019699:C:CCdonor_gain1.0000
2:206019715:T:Adonor_gain1.0000
2:206019841:TTATG:Tacceptor_gain1.0000
2:206019842:TATG:Tacceptor_gain1.0000
2:206019843:ATG:Aacceptor_gain1.0000
2:206019844:TG:Tacceptor_gain1.0000
2:206019844:TGC:Tacceptor_loss1.0000
2:206019846:C:CCacceptor_gain1.0000
2:206019846:CTAAG:Cacceptor_loss1.0000
2:206019847:T:Cacceptor_loss1.0000
2:206028105:TCTAA:Tdonor_loss1.0000
2:206028106:CTAAC:Cdonor_loss1.0000
2:206028107:TAA:Tdonor_loss1.0000
2:206028108:AAC:Adonor_loss1.0000
2:206028110:C:CGdonor_loss1.0000
2:206028331:CTGAC:Cacceptor_gain1.0000
2:206028343:G:Cacceptor_gain1.0000
2:206028343:G:GCacceptor_gain1.0000
2:206046497:GACTT:Gdonor_loss1.0000
2:206046499:CTTAC:Cdonor_loss1.0000

AlphaMissense

6735 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:206005488:A:GL655P1.000
2:206017692:A:CH510Q1.000
2:206017692:A:TH510Q1.000
2:206017701:A:CC507W1.000
2:206017702:C:AC507F1.000
2:206017702:C:GC507S1.000
2:206017702:C:TC507Y1.000
2:206017703:A:GC507R1.000
2:206017703:A:TC507S1.000
2:206017743:G:CC493W1.000
2:206017744:C:GC493S1.000
2:206017744:C:TC493Y1.000
2:206017745:A:GC493R1.000
2:206017745:A:TC493S1.000
2:206017761:A:CF487L1.000
2:206017761:A:TF487L1.000
2:206017762:A:CF487C1.000
2:206017762:A:GF487S1.000
2:206017763:A:GF487L1.000
2:206017768:G:TA485D1.000
2:206017773:G:CC483W1.000
2:206017774:C:GC483S1.000
2:206017774:C:TC483Y1.000
2:206017775:A:GC483R1.000
2:206017775:A:TC483S1.000
2:206056928:G:CH78Q1.000
2:206056928:G:TH78Q1.000
2:206056929:T:CH78R1.000
2:206056930:G:AH78Y1.000
2:206056930:G:CH78D1.000

dbSNP variants (sampled 300 via entrez): RS1000023869 (2:206000500 G>T), RS1000060084 (2:206005846 T>C), RS1000118195 (2:206000302 T>C,G), RS1000146949 (2:206085560 G>A), RS1000148194 (2:206045400 A>G), RS1000213995 (2:206043608 C>A,T), RS1000287065 (2:206021426 C>G), RS1000313870 (2:206046886 T>C), RS1000345622 (2:206076981 C>A,G), RS1000386590 (2:206081137 T>C), RS1000398387 (2:206070206 A>T), RS1000401492 (2:206025371 T>C), RS1000434964 (2:206045675 A>G), RS1000439000 (2:206027975 G>A,T), RS1000458790 (2:206076710 C>T)

Disease associations

OMIM: gene MIM:619207 | disease phenotypes:

GenCC curated gene-disease

Mondo (1): megacolon (MONDO:0001273)

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000426_9Obesity (extreme)8.000000e-06
GCST004619_200Reticulocyte fraction of red cells8.000000e-09
GCST005951_45Body mass index1.000000e-09
GCST007565_91Morning person1.000000e-13
GCST007576_291Chronotype1.000000e-13
GCST011494_17Daytime nap4.000000e-12
GCST90020024_1166A body shape index4.000000e-09
GCST90020029_853Waist circumference adjusted for body mass index2.000000e-08

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0007986reticulocyte count
EFO:0004340body mass index
EFO:0008328chronotype measurement
EFO:0007828daytime rest measurement
EFO:0007789BMI-adjusted waist circumference

MeSH disease descriptors (1)

DescriptorNameTree numbers
D008531MegacolonC06.405.469.158.701

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

37 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression5
mercuric bromidedecreases expression, affects cotreatment2
Cisplatinaffects cotreatment, decreases expression2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
aristolochic acid Idecreases expression1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
FR900359increases phosphorylation1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
trichostatin Aaffects expression1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
entinostatdecreases expression1
scriptaiddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
torcetrapibincreases expression1
dorsomorphinaffects cotreatment, decreases expression1
suberoyl bis-hydroxamic aciddecreases expression1
jinfukangaffects cotreatment, decreases expression1
Vorinostatdecreases expression1
Acetaminophendecreases expression1
Cadmiumdecreases expression, increases abundance1
Caffeinedecreases phosphorylation1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Methyl Methanesulfonateincreases expression1
Rifampindecreases expression1
Dronabinolincreases expression1
Thimerosalincreases expression1

Clinical trials (associated diseases)

2 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04340856Not specifiedCOMPLETEDRetrospective, Uncontrolled Cohort Study on the Therapy of Chronic Megalon
NCT07470892Not specifiedNOT_YET_RECRUITINGPreoperative Fish Oil PN and Prognosis After Constipation Surgery
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): megacolon