◎ Sugi Atlas

Atlas / Gene / WDR70

WDR70

gene
On this page

Also known as FLJ10233

Summary

WDR70 (WD repeat domain 70, HGNC:25495) is a protein-coding gene on chromosome 5p13.2, encoding WD repeat-containing protein 70 (Q9NW82). It is a common-essential gene (DepMap: required in 99.7% of cancer cell lines).

Enables enzyme binding activity. Predicted to be located in nucleoplasm. Predicted to be active in nucleus and site of double-strand break.

Source: NCBI Gene 55100 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 89 total
  • Cancer dependency (DepMap): dependent in 99.7% of screened cell lines (common-essential)
  • MANE Select transcript: NM_018034

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25495
Approved symbolWDR70
NameWD repeat domain 70
Location5p13.2
Locus typegene with protein product
StatusApproved
AliasesFLJ10233
Ensembl geneENSG00000082068
Ensembl biotypeprotein_coding
OMIM617233
Entrez55100

Gene structure

Transcript identifiers

Ensembl transcripts: 13 — 8 protein_coding, 4 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000265107, ENST00000504564, ENST00000505799, ENST00000507136, ENST00000508730, ENST00000510699, ENST00000511906, ENST00000863540, ENST00000863541, ENST00000863542, ENST00000928085, ENST00000928086, ENST00000941054

RefSeq mRNA: 3 — MANE Select: NM_018034 NM_001345998, NM_001345999, NM_018034

CCDS: CCDS34147

Canonical transcript exons

ENST00000265107 — 18 exons

ExonStartEnd
ENSE000010062823772111537721215
ENSE000010062853772285537722934
ENSE000020510403775248637753435
ENSE000020562843737931837379392
ENSE000034659933738160237381685
ENSE000034700283739200037392120
ENSE000034725483744323937443372
ENSE000034759253739637537396570
ENSE000034783693737948937379554
ENSE000034902153772688337727045
ENSE000034963133743792237437981
ENSE000035128773770294937703087
ENSE000035768833760506437605238
ENSE000035868133770105837701142
ENSE000036121913769765537697754
ENSE000036127283772493437725050
ENSE000036189133751651437516590
ENSE000036423973747983437479987

Expression profiles

Bgee: expression breadth ubiquitous, 270 present calls, max score 94.89.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.1894 / max 275.0111, expressed in 1807 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
5617617.57611799
561751.5631941
2035261.0502666

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548894.89gold quality
calcaneal tendonUBERON:000370192.44gold quality
cortical plateUBERON:000534392.34gold quality
ganglionic eminenceUBERON:000402392.31gold quality
oocyteCL:000002391.40gold quality
ventricular zoneUBERON:000305390.56gold quality
granulocyteCL:000009490.47gold quality
hindlimb stylopod muscleUBERON:000425289.85gold quality
muscle layer of sigmoid colonUBERON:003580589.79gold quality
ectocervixUBERON:001224989.76gold quality
gastrocnemiusUBERON:000138889.61gold quality
tibial nerveUBERON:000132389.51gold quality
endocervixUBERON:000045889.50gold quality
muscle of legUBERON:000138389.39gold quality
tibial arteryUBERON:000761089.25gold quality
popliteal arteryUBERON:000225089.24gold quality
olfactory segment of nasal mucosaUBERON:000538689.06gold quality
body of uterusUBERON:000985388.98gold quality
right ovaryUBERON:000211888.87gold quality
left ovaryUBERON:000211988.75gold quality
lower esophagus muscularis layerUBERON:003583388.73gold quality
tendonUBERON:000004388.72gold quality
lower esophagusUBERON:001347388.72gold quality
esophagogastric junction muscularis propriaUBERON:003584188.69gold quality
skin of legUBERON:000151188.62gold quality
skin of abdomenUBERON:000141688.44gold quality
aortaUBERON:000094788.35gold quality
secondary oocyteCL:000065588.29gold quality
embryoUBERON:000092288.25gold quality
lower esophagus mucosaUBERON:003583488.22gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.67

Regulation

Is transcription factor: no

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 99.7% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 3)

  • CRL4(Wdr70) regulates H2B monoubiquitination and facilitates Exo1-dependent DNA repair resection. (PMID:27098497)
  • Ovarian cancer had different expression of WDR70 and H2B monoubiquitination compared with normal tissue (PMID:29130659)
  • Requirement of WDR70 for POLE3-mediated DNA double-strand breaks repair. (PMID:37682991)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioWDR70ENSDARG00000109022
mus_musculusWdr70ENSMUSG00000039828
rattus_norvegicusWdr70ENSRNOG00000013336
drosophila_melanogasterCG5543FBGN0034908
caenorhabditis_elegansWBGENE00001513

Protein

Protein identifiers

WD repeat-containing protein 70 — Q9NW82 (reviewed: Q9NW82)

All UniProt accessions (2): Q9NW82, D6RIW8

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the WD repeat GAD-1 family.

RefSeq proteins (3): NP_001332927, NP_001332928, NP_060504* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR051858WD_repeat_GAD-1Family

Pfam: PF00400

UniProt features (57 total): strand 31, repeat 7, compositionally biased region 6, region of interest 4, modified residue 4, cross-link 3, chain 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDBMethodResolution (Å)
6ZYMELECTRON MICROSCOPY3.4
8I0WELECTRON MICROSCOPY3.4
7A5PELECTRON MICROSCOPY5

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NW82-F178.370.47

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 (7): 452, 579, 621, 638, 296, 590, 596

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-72163mRNA Splicing - Major Pathway

MSigDB gene sets: 85 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_MCMV_INFECTION_UP, DARWICHE_SKIN_TUMOR_PROMOTER_DN, DARWICHE_PAPILLOMA_RISK_LOW_UP, DARWICHE_PAPILLOMA_RISK_HIGH_DN, DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN, REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA, GOBP_RNA_SPLICING, REACTOME_MRNA_SPLICING, GCM_NF2, REACTOME_METABOLISM_OF_RNA, GOCC_U2_TYPE_SPLICEOSOMAL_COMPLEX, BENPORATH_OCT4_TARGETS, GOCC_SPLICEOSOMAL_COMPLEX, GOCC_RIBONUCLEOPROTEIN_COMPLEX, GOCC_SITE_OF_DOUBLE_STRAND_BREAK

GO Biological Process (0):

GO Molecular Function (2): enzyme binding (GO:0019899), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), site of double-strand break (GO:0035861)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
mRNA Splicing1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein binding1
binding1
intracellular membrane-bounded organelle1
nuclear lumen1
cellular anatomical structure1
site of DNA damage1

Protein interactions and networks

STRING

956 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
WDR70NUP155O75694939
WDR70CPLANE1Q9H799934
WDR70NIPBLQ6KC79833
WDR70SLC1A3P43003697
WDR70TMEM267Q0VDI3570
WDR70CCDC152Q4G0S7461
WDR70CRNKL1Q9BZJ0460
WDR70HDHD2Q9H0R4460
WDR70BUD31P41223453
WDR70ZNF280DQ6N043453
WDR70RNF216Q9NWF9434
WDR70LMBRD2Q68DH5433
WDR70DHX8Q14562431
WDR70DHX38Q92620422
WDR70SART1O43290421

IntAct

62 interactions, top by confidence:

ABTypeScore
RBPJNOTCH1psi-mi:“MI:0914”(association)0.910
CCT2TXNDC9psi-mi:“MI:0914”(association)0.730
PDCL3PEX7psi-mi:“MI:0914”(association)0.640
CCT3TXNDC9psi-mi:“MI:0914”(association)0.640
CCT5TXNDC9psi-mi:“MI:0914”(association)0.640
CCT7TXNDC9psi-mi:“MI:0914”(association)0.640
TCEANC2HTATSF1psi-mi:“MI:0914”(association)0.530
ZNRD2CCDC85Cpsi-mi:“MI:0914”(association)0.530
WDR70CDC37psi-mi:“MI:0915”(physical association)0.400
CHORDC1SSR3psi-mi:“MI:0914”(association)0.350
Ccdc12PLRG1psi-mi:“MI:0914”(association)0.350
Tecpr2PUF60psi-mi:“MI:0914”(association)0.350
Klc3ZC3HAV1psi-mi:“MI:0914”(association)0.350
RBPJRPA2psi-mi:“MI:0914”(association)0.350
Xpo1IFT56psi-mi:“MI:0914”(association)0.350
CCT3C6orf11psi-mi:“MI:0914”(association)0.350
CCT7C6orf11psi-mi:“MI:0914”(association)0.350
RBPJZNF268psi-mi:“MI:0914”(association)0.350
TCEANC2ANKHD1psi-mi:“MI:0914”(association)0.350
ARRB2AHCYL1psi-mi:“MI:0914”(association)0.350
WDR48UNC13Bpsi-mi:“MI:0914”(association)0.350
SYT2ARHGAP10psi-mi:“MI:0914”(association)0.350
CCT2WDR91psi-mi:“MI:0914”(association)0.350
PLCD3AP3B1psi-mi:“MI:0914”(association)0.350
CCT5TUBAL3psi-mi:“MI:0914”(association)0.350
CCT3TUBAL3psi-mi:“MI:0914”(association)0.350
CCT7WDR46psi-mi:“MI:0914”(association)0.350
RASA2DKC1psi-mi:“MI:0914”(association)0.350

BioGRID (111): WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Biochemical Activity), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), WDR70 (Affinity Capture-MS), PRPF38A (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTH9, A6QQM4, A7SKE9, B4KLC0, B4LRY2, B4Q5Z1, E0X9N4, O60308, P0CR50, P0CR51, P10711, P23193, Q02336, Q09464, Q0VA16, Q15560, Q17CJ5, Q1HE00, Q28CY2, Q29RL9, Q3B7L8, Q3EA33, Q4KLL0, Q4R4J1, Q4V7D7, Q5EB92, Q5RAY5, Q5U2P3, Q5ZM16, Q63799, Q641B2, Q6DJI8, Q6DRC4, Q6GPP0, Q6IDS6, Q6NZZ9, Q6P616, Q7QJV0, Q7ZXB5, Q8BHS3

Diamond homologs: A8IZG4, O16519, P38129, P39706, Q0VA16, Q32LB0, Q3TWF6, Q55DA2, Q5EB92, Q6BYU4, Q6GPP0, Q7K0L4, Q7KWL3, Q9NW82, Q9W1J3, A4QNE6, O42478, P16371, P32330, Q04725, Q04727, Q07141, Q55AR8, Q5M7F6, Q62441, Q9UT73, Q9WVB2, Q7ZXZ2

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 81 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
Formation of tubulin folding intermediates by CCT/TriC536.5×2e-05
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding535.2×2e-05
Chaperonin-mediated protein folding525.9×6e-05
Protein folding522.4×1e-04
Signaling by BRAF and RAF1 fusions617.6×6e-05
mRNA Polyadenylation913.6×3e-06
mRNA Splicing - Major Pathway1312.2×1e-08
mRNA Splicing59.5×4e-03

GO biological processes:

GO termPartnersFoldFDR
positive regulation of telomere maintenance via telomerase553.1×8e-06
mRNA splicing, via spliceosome911.9×8e-06
protein folding710.5×4e-04
mRNA processing89.1×3e-04
RNA splicing78.9×9e-04
protein stabilization87.8×7e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance62
Likely benign4
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

4351 predictions. Top by Δscore:

VariantEffectΔscore
5:37379481:T:Aacceptor_gain1.0000
5:37379487:A:AGacceptor_gain1.0000
5:37379488:G:GGacceptor_gain1.0000
5:37381593:AT:Aacceptor_gain1.0000
5:37381594:T:Gacceptor_gain1.0000
5:37381594:T:TAacceptor_gain1.0000
5:37381598:TTAG:Tacceptor_loss1.0000
5:37381599:TAGGT:Tacceptor_loss1.0000
5:37381600:A:AGacceptor_gain1.0000
5:37381600:AG:Aacceptor_gain1.0000
5:37381601:G:GGacceptor_gain1.0000
5:37381601:GG:Gacceptor_gain1.0000
5:37381601:GGT:Gacceptor_gain1.0000
5:37381601:GGTA:Gacceptor_gain1.0000
5:37381601:GGTAA:Gacceptor_gain1.0000
5:37381681:ACTGG:Adonor_gain1.0000
5:37381682:CTGG:Cdonor_gain1.0000
5:37381682:CTGGG:Cdonor_loss1.0000
5:37381683:TGG:Tdonor_gain1.0000
5:37381683:TGGG:Tdonor_loss1.0000
5:37381684:GG:Gdonor_gain1.0000
5:37381684:GGG:Gdonor_gain1.0000
5:37381684:GGGT:Gdonor_loss1.0000
5:37381685:GG:Gdonor_gain1.0000
5:37381685:GGTAA:Gdonor_loss1.0000
5:37381686:G:GGdonor_gain1.0000
5:37381686:GTAAG:Gdonor_loss1.0000
5:37381687:T:Gdonor_loss1.0000
5:37391989:A:AGacceptor_gain1.0000
5:37391995:TTCA:Tacceptor_loss1.0000

AlphaMissense

4328 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:37381619:T:CF37L1.000
5:37381621:T:AF37L1.000
5:37381621:T:GF37L1.000
5:37381658:G:CA50P1.000
5:37381659:C:AA50D1.000
5:37443266:G:CG194R1.000
5:37443267:G:AG194D1.000
5:37443272:C:AR196S1.000
5:37443285:G:AG200E1.000
5:37443311:T:AW209R1.000
5:37443311:T:CW209R1.000
5:37443314:G:CD210H1.000
5:37443315:A:CD210A1.000
5:37443315:A:GD210G1.000
5:37443315:A:TD210V1.000
5:37443316:T:AD210E1.000
5:37443316:T:GD210E1.000
5:37443321:C:AA212D1.000
5:37443324:G:AG213E1.000
5:37443347:T:CF221L1.000
5:37443348:T:GF221C1.000
5:37443349:T:AF221L1.000
5:37443349:T:GF221L1.000
5:37479881:T:CL245P1.000
5:37479921:A:CR258S1.000
5:37479921:A:TR258S1.000
5:37479925:G:CG260R1.000
5:37479926:G:AG260D1.000
5:37479952:G:AG269R1.000
5:37479952:G:CG269R1.000

dbSNP variants (sampled 300 via entrez): RS1000003126 (5:37451735 G>A), RS1000003541 (5:37480024 A>G), RS1000019951 (5:37694696 G>A,C,T), RS1000025834 (5:37592388 G>C), RS1000026556 (5:37741714 A>G), RS1000036527 (5:37559541 G>A), RS1000055909 (5:37552063 C>A), RS1000060440 (5:37538451 A>G), RS1000067381 (5:37748196 A>G), RS1000071263 (5:37574340 A>G), RS1000074952 (5:37684183 G>C,T), RS1000080807 (5:37701525 C>A,T), RS1000087827 (5:37389086 A>C,G,T), RS1000090086 (5:37434972 T>G), RS1000115803 (5:37415156 A>C)

Disease associations

OMIM: gene MIM:617233 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST006479_116Diverticular disease1.000000e-11
GCST008152_165Weight7.000000e-06
GCST008163_551Height4.000000e-08
GCST008163_630Height9.000000e-06
GCST010143_4Meat-related diet5.000000e-08
GCST010316_3Serum docosahexaenoic fatty acid concentration in metabolic syndrome4.000000e-06
GCST010318_7Serum omega-3 polyunsaturated fatty acid concentration in metabolic syndrome3.000000e-06
GCST010725_6Malaria9.000000e-07
GCST010725_66Malaria1.000000e-06
GCST010725_85Malaria5.000000e-06
GCST011696_6Alzheimer’s disease2.000000e-07
GCST90025872_6Chronic widespread musculoskeletal pain8.000000e-07

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0009959diverticular disease
EFO:0004338body weight
EFO:0008111diet measurement
EFO:0007761docosahexaenoic acid measurement
EFO:0010119omega-3 polyunsaturated fatty acid measurement
EFO:0010099chronic widespread pain

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases expression, increases methylation6
potassium chromate(VI)affects cotreatment, decreases expression, increases expression2
Cisplatinincreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideaffects expression, decreases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
TAK-243increases sumoylation1
dicrotophosdecreases expression1
arseniteaffects binding, increases reaction1
benzo(e)pyrenedecreases methylation1
aflatoxin B2decreases methylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent ionaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
LDN 193189affects cotreatment, increases expression1
4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acidincreases expression1
Doxorubicindecreases expression1
Enzyme Inhibitorsincreases O-linked glycosylation, decreases activity1
Ivermectindecreases expression1
Methapyrilenedecreases methylation1
Methyl Methanesulfonateincreases expression1
Phthalic Acidsdecreases methylation1
Valproic Aciddecreases expression1
Aflatoxin B1increases methylation1
Cadmium Chlorideincreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.4
BioBTree
v2.0.2

Sources 75

This page pulls from 75 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomereactomeparentrefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot