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WDR7

gene
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Also known as KIAA0541TRAG

Summary

WDR7 (WD repeat domain 7, HGNC:13490) is a protein-coding gene on chromosome 18q21.31, encoding WD repeat-containing protein 7 (Q9Y4E6). It is a selective cancer dependency (DepMap: 80.1% of cell lines).

This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD) that may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. The encoded protein forms the beta subunit of rabconnectin-3 and binds directly with Rab3A GDP/GTP exchange protein and indirectly with Rab3A GDP/GTP activating protein; these proteins are regulators of Rab3 small G protein family members involved in control of the calcium-dependant exocytosis of neurotransmitters. Alternatively spliced transcript variants encoding different isoforms have been described.

Source: NCBI Gene 23335 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 211 total
  • Cancer dependency (DepMap): dependent in 80.1% of screened cell lines
  • MANE Select transcript: NM_015285

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:13490
Approved symbolWDR7
NameWD repeat domain 7
Location18q21.31
Locus typegene with protein product
StatusApproved
AliasesKIAA0541, TRAG
Ensembl geneENSG00000091157
Ensembl biotypeprotein_coding
OMIM613473
Entrez23335

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 5 protein_coding, 4 protein_coding_CDS_not_defined, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000254442, ENST00000357574, ENST00000585669, ENST00000585754, ENST00000585824, ENST00000586124, ENST00000587403, ENST00000589935, ENST00000590557, ENST00000591449, ENST00000591524, ENST00000593058

RefSeq mRNA: 4 — MANE Select: NM_015285 NM_001382485, NM_001382487, NM_015285, NM_052834

CCDS: CCDS11962, CCDS11963

Canonical transcript exons

ENST00000254442 — 28 exons

ExonStartEnd
ENSE000006695805675658356757352
ENSE000006695865681603156816144
ENSE000009033685667249756672674
ENSE000009033695667933256679438
ENSE000009033705668131356681391
ENSE000009033715668267956682853
ENSE000009033725668595656686032
ENSE000009033735669121656691361
ENSE000009033745669171556691817
ENSE000009033795677678256776880
ENSE000009033815678153356781656
ENSE000009033825687994456880165
ENSE000009033885702074557020849
ENSE000011063775671796456718159
ENSE000011063885668685556686974
ENSE000011601735669624256696462
ENSE000011601885669461956694760
ENSE000035120285677943156779549
ENSE000035710825669495056695198
ENSE000035744825673138356731597
ENSE000035831965693853356938682
ENSE000035994855696243056962529
ENSE000036168815693931156939393
ENSE000036655285675886556758953
ENSE000037331875702700457029792
ENSE000037453765693578856935905
ENSE000037471935692392256924108
ENSE000039096495665135956651576

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.1048 / max 172.2434, expressed in 1764 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
17033710.95031744
1703402.5035591
1703391.4078683
1703380.180665
1703410.032517
1703420.030116

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
endothelial cellCL:000011598.31gold quality
middle temporal gyrusUBERON:000277197.79gold quality
Brodmann (1909) area 23UBERON:001355497.26gold quality
Brodmann (1909) area 10UBERON:001354197.07gold quality
frontal poleUBERON:000279597.03gold quality
postcentral gyrusUBERON:000258195.09gold quality
lateral nuclear group of thalamusUBERON:000273695.07gold quality
parietal lobeUBERON:000187294.74gold quality
orbitofrontal cortexUBERON:000416794.51gold quality
ponsUBERON:000098894.32gold quality
superior frontal gyrusUBERON:000266194.32gold quality
CA1 field of hippocampusUBERON:000388194.08gold quality
Brodmann (1909) area 46UBERON:000648394.07gold quality
entorhinal cortexUBERON:000272893.97gold quality
corpus callosumUBERON:000233693.68gold quality
paraflocculusUBERON:000535193.39gold quality
middle frontal gyrusUBERON:000270293.37gold quality
substantia nigra pars compactaUBERON:000196593.32gold quality
calcaneal tendonUBERON:000370192.94gold quality
cerebellar vermisUBERON:000472092.80gold quality
superior vestibular nucleusUBERON:000722792.70gold quality
choroid plexus epitheliumUBERON:000391192.48gold quality
primary visual cortexUBERON:000243692.44gold quality
occipital lobeUBERON:000202192.18gold quality
substantia nigra pars reticulataUBERON:000196692.05gold quality
prefrontal cortexUBERON:000045191.64gold quality
medulla oblongataUBERON:000189691.34gold quality
dorsal motor nucleus of vagus nerveUBERON:000287091.29gold quality
lateral globus pallidusUBERON:000247691.28gold quality
inferior olivary complexUBERON:000212790.90gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-GEOD-124858no191.30
E-ANND-3no7.32

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): BRD1

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 80.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • Evolution of a Human-Specific Tandem Repeat Associated with ALS. (PMID:32750315)

Cross-species orthologs

7 orthologs

OrganismSymbolGene ID
danio_rerioWDR7ENSDARG00000100274
danio_rerioENSDARG00000107858
danio_rerioENSDARG00000112868
mus_musculusWdr7ENSMUSG00000040560
rattus_norvegicusWdr7ENSRNOG00000018387
drosophila_melanogasterRbcn-3BFBGN0023510
caenorhabditis_elegansWBGENE00004314

Paralogs (26): PAFAH1B1 (ENSG00000007168), SNRNP40 (ENSG00000060688), WDR62 (ENSG00000075702), TBL2 (ENSG00000106638), PAK1IP1 (ENSG00000111845), WDR75 (ENSG00000115368), DCAF4 (ENSG00000119599), DAW1 (ENSG00000123977), TEP1 (ENSG00000129566), AHI1 (ENSG00000135541), WDR38 (ENSG00000136918), MAPKBP1 (ENSG00000137802), POC1B (ENSG00000139323), NEDD1 (ENSG00000139350), COP1 (ENSG00000143207), WDR17 (ENSG00000150627), WDR43 (ENSG00000163811), POC1A (ENSG00000164087), WDR88 (ENSG00000166359), WDR81 (ENSG00000167716), DCAF4L2 (ENSG00000176566), DCAF4L1 (ENSG00000182308), WDR27 (ENSG00000184465), NWD1 (ENSG00000188039), WDR5 (ENSG00000196363), WDR5B (ENSG00000196981)

Protein

Protein identifiers

WD repeat-containing protein 7 — Q9Y4E6 (reviewed: Q9Y4E6)

Alternative names: Rabconnectin-3 beta, TGF-beta resistance-associated protein TRAG

All UniProt accessions (5): Q9Y4E6, K7EMB8, K7EMF3, K7EPQ4, K7EPY9

Isoforms (2)

UniProt IDNamesCanonical?
Q9Y4E6-11yes
Q9Y4E6-22

RefSeq proteins (4): NP_001369414, NP_001369416, NP_056100, NP_443066 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR011047Quinoprotein_ADH-like_sfHomologous_superfamily
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019775WD40_repeat_CSConserved_site
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR049916WDR72-likeFamily
IPR057848WDR72_alpha-solDomain

Pfam: PF00400, PF23123

UniProt features (18 total): repeat 9, region of interest 2, compositionally biased region 2, modified residue 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y4E6-F174.310.36

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): 935, 1456

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 178 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR, MODULE_66, GOBP_VACUOLAR_ACIDIFICATION, DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN, SCHLOSSER_SERUM_RESPONSE_DN, HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP, MODULE_88, GOBP_REGULATION_OF_PH, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_MONOATOMIC_ION_HOMEOSTASIS, MODULE_6, MODULE_11, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN

GO Biological Process (1): hematopoietic progenitor cell differentiation (GO:0002244)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
hemopoiesis1
cell differentiation1
binding1
intracellular anatomical structure1
cellular anatomical structure1

Protein interactions and networks

STRING

1850 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
WDR7DMXL2Q8TDJ6978
WDR7NCOR2Q9Y618856
WDR7RAB3GAP2Q9H2M9832
WDR7MADDQ8WXG6808
WDR7RAB3AP20336791
WDR7VMA22Q96NT0738
WDR7DNAJC5Q9H3Z4641
WDR7ATP6V1C1P21283576
WDR7ROGDIQ9GZN7560
WDR7DMXL1Q9Y485545
WDR7ATP6V1HQ9UI12534
WDR7TSNAXQ99598514
WDR7ATP6V1E1P36543511
WDR7DNAJC28Q9NX36469
WDR7SGMS1Q86VZ5462

IntAct

26 interactions, top by confidence:

ABTypeScore
BNIP1NBASpsi-mi:“MI:0914”(association)0.640
ATP6V1C2ATP6V1G1psi-mi:“MI:0914”(association)0.640
ATP6V1B2ATP6V1G1psi-mi:“MI:0914”(association)0.530
RPN1APBB1psi-mi:“MI:0914”(association)0.530
ZNRD2MYO9Apsi-mi:“MI:0914”(association)0.530
ATP6V1G2ATP6V1B1psi-mi:“MI:0914”(association)0.530
SFPQWDR7psi-mi:“MI:0915”(physical association)0.400
RYBPFAM186Apsi-mi:“MI:0914”(association)0.350
MAPTSHTN1psi-mi:“MI:0914”(association)0.350
ITM2BILVBLpsi-mi:“MI:0914”(association)0.350
ATP6V1E1ATP6V1Dpsi-mi:“MI:0914”(association)0.350
ATP6V1FMID1psi-mi:“MI:0914”(association)0.350
ATP6V1G1MRPL3psi-mi:“MI:0914”(association)0.350
ATP6V1HATP6V1G1psi-mi:“MI:0914”(association)0.350
DDOSTATL3psi-mi:“MI:0914”(association)0.350
OST4ATL3psi-mi:“MI:0914”(association)0.350
DMXL1LLGL1psi-mi:“MI:0914”(association)0.350
WDR7DMXL2psi-mi:“MI:0914”(association)0.350
atp6v1g_humanHSPA8psi-mi:“MI:0914”(association)0.350
UGGT2MAP2K7psi-mi:“MI:0914”(association)0.350
ROGDIATP2A1psi-mi:“MI:0914”(association)0.350
ROGDINUDT3psi-mi:“MI:0914”(association)0.350
TGOLN2BLTP3Bpsi-mi:“MI:2364”(proximity)0.270

BioGRID (103): FRMD6 (Two-hybrid), WDR7 (Affinity Capture-MS), WDR7 (Affinity Capture-MS), WDR7 (Affinity Capture-MS), WDR7 (Affinity Capture-MS), WDR7 (Affinity Capture-MS), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic), WDR7 (Negative Genetic)

ESM2 similar proteins: A0A0G2KIZ8, A0A1L8GXY4, A0A571BF63, A0A8M9QN10, A2CEI4, A2RRP1, A4D1P6, A6H8T2, A9X1C6, B0FXQ5, B1WC10, B2KIQ4, B2RY71, B2RYI0, B7FF09, B7FF12, E9PYY5, F1QHZ6, Q1LXZ7, Q2HJE1, Q3UMY5, Q402B2, Q4V8G4, Q5R6T6, Q5RE88, Q5U1Z0, Q5VTH9, Q5XIZ9, Q5ZLL7, Q6DFC6, Q6DTM3, Q6GPB9, Q6P2C0, Q6TEN6, Q7TMQ7, Q7ZVR1, Q8BMG7, Q8BX17, Q8C147, Q8IWG1

Diamond homologs: D3YYM4, Q3MJ13, Q5RFQ4, Q920I9, Q9ERH3, Q9Y4E6, A2QEV8, A4HUV2, B0XYC8, B6GZD3, F4IH25, O42858, O43071, P25382, P39706, P41838, Q00808, Q05AM5, Q08924, Q26544, Q2UQ34, Q32LN7, Q4P5F5, Q4QH39, Q4V7A0, Q4WX90, Q54KL5, Q54S59, Q5B464, Q5B8Y3, Q5ZJH5, Q6GMD2, Q6P5M2, Q6PBD6, Q7KWK5, Q93847, Q9ERF3, Q9GZS3

SIGNOR signaling

1 interactions.

AEffectBMechanism
WDR7“form complex”“RAVE complex, DMXL1 variant”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 39 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
Regulation of MITF-M-dependent genes involved in lysosome biogenesis and autophagy6134.3×8e-11
Insulin receptor recycling9114.2×3e-15
Transferrin endocytosis and recycling9110.5×3e-15
ROS and RNS production in phagocytes9100.8×6e-15
Amino acids regulate mTORC1960.1×7e-13
Ion channel transport1032.0×1e-11

GO biological processes:

GO termPartnersFoldFDR
synaptic vesicle lumen acidification7187.2×7e-13
vacuolar acidification7146.5×3e-12
regulation of macroautophagy867.6×2e-11
proton transmembrane transport653.5×7e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance177
Likely benign6
Benign5

Top pathogenic / likely-pathogenic (0)

SpliceAI

6910 predictions. Top by Δscore:

VariantEffectΔscore
18:56651573:ACAGG:Adonor_loss1.0000
18:56651574:CAGGT:Cdonor_loss1.0000
18:56651575:AGGT:Adonor_loss1.0000
18:56651576:GGTAA:Gdonor_loss1.0000
18:56651577:GTAA:Gdonor_loss1.0000
18:56651578:T:Adonor_loss1.0000
18:56672491:TTTCA:Tacceptor_loss1.0000
18:56672492:TTCA:Tacceptor_loss1.0000
18:56672493:TCA:Tacceptor_loss1.0000
18:56672494:CA:Cacceptor_loss1.0000
18:56672495:A:AGacceptor_gain1.0000
18:56672495:A:Tacceptor_loss1.0000
18:56672496:G:GGacceptor_gain1.0000
18:56672496:G:GTacceptor_loss1.0000
18:56672671:GCAA:Gdonor_gain1.0000
18:56672675:G:GGdonor_gain1.0000
18:56672679:G:GGdonor_gain1.0000
18:56679435:GTGG:Gdonor_gain1.0000
18:56679437:GG:Gdonor_gain1.0000
18:56679438:GG:Gdonor_gain1.0000
18:56681070:G:GTdonor_gain1.0000
18:56681071:A:Tdonor_gain1.0000
18:56682666:G:Aacceptor_gain1.0000
18:56682669:A:AGacceptor_gain1.0000
18:56682669:AT:Aacceptor_gain1.0000
18:56682670:T:Gacceptor_gain1.0000
18:56682670:T:TAacceptor_gain1.0000
18:56682674:T:Gacceptor_gain1.0000
18:56682674:TGTA:Tacceptor_loss1.0000
18:56682677:A:AGacceptor_gain1.0000

AlphaMissense

9705 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
18:56672552:T:AW13R1.000
18:56672552:T:CW13R1.000
18:56679422:A:CS84R1.000
18:56679424:T:AS84R1.000
18:56679424:T:GS84R1.000
18:56681326:T:AW94R1.000
18:56681326:T:CW94R1.000
18:56681349:T:GC101W1.000
18:56686000:T:AW189R1.000
18:56686000:T:CW189R1.000
18:56695103:T:CL421P1.000
18:56695115:G:CR425P1.000
18:56695169:T:CL443P1.000
18:56696244:T:AW454R1.000
18:56696244:T:CW454R1.000
18:56696338:T:CL485P1.000
18:56696347:G:AG488E1.000
18:56696373:T:AW497R1.000
18:56696373:T:CW497R1.000
18:56718001:A:TD539V1.000
18:56718006:T:CS541P1.000
18:56718087:T:AW568R1.000
18:56718087:T:CW568R1.000
18:56718109:T:CL575P1.000
18:56718142:T:AV586D1.000
18:56718144:T:AW587R1.000
18:56718144:T:CW587R1.000
18:56718146:G:CW587C1.000
18:56718146:G:TW587C1.000
18:56731395:G:CR596P1.000

dbSNP variants (sampled 300 via entrez): RS1000004806 (18:56825556 G>C), RS1000010219 (18:56709820 C>T), RS1000011211 (18:57000632 A>T), RS1000015725 (18:56842861 G>A,C), RS1000030730 (18:56754397 A>C,G), RS1000045450 (18:56682569 A>C), RS1000045955 (18:56663360 A>C), RS1000061669 (18:56795648 A>G), RS1000071464 (18:56897374 A>C,G), RS1000077806 (18:57020934 G>A,C,T), RS1000078412 (18:56949556 G>A,T), RS1000079316 (18:56667182 T>C), RS1000082595 (18:56890553 A>G), RS1000089026 (18:56842565 C>T), RS1000097932 (18:56812117 T>C)

Disease associations

OMIM: gene MIM:613473 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000267_2Multiple sclerosis (age of onset)4.000000e-06
GCST001313_6Depression and alcohol dependence8.000000e-06
GCST002682_14Tourette’s syndrome or obsessive-compulsive disorder4.000000e-06
GCST006624_123Systolic blood pressure3.000000e-17
GCST009379_221Type 2 diabetes3.000000e-08
GCST011985_5Congenital heart disease (septal defects)2.000000e-08
GCST012490_109Femur bone mineral density x serum urate levels interaction1.000000e-08
GCST012490_270Femur bone mineral density x serum urate levels interaction2.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004847age at onset
EFO:0006335systolic blood pressure
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs501415WDR70.000

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression6
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression3
potassium chromate(VI)affects cotreatment, decreases expression2
Acetaminophendecreases expression, increases expression2
Aflatoxin B1affects expression, increases methylation2
Cadmium Chloridedecreases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
chloroacetaldehydedecreases expression1
triphenyl phosphateaffects expression1
beta-lapachonedecreases expression1
sodium arseniteincreases expression1
aflatoxin B2decreases methylation1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression1
deguelindecreases expression1
(+)-JQ1 compoundincreases expression1
Rosiglitazonedecreases expression1
Arsenic Trioxideincreases response to substance1
Antimycin Adecreases expression1
Atrazinedecreases expression1
Caffeineaffects phosphorylation1
Diazinonincreases methylation1
Ivermectinaffects expression1
Oxygendecreases expression1
Quercetindecreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
Valproic Acidincreases expression1

Clinical trials (associated diseases)

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

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
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Sources 74

This page pulls from 74 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_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot