WDTC1

gene
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Also known as KIAA1037ADPDCAF9

Summary

WDTC1 (WD and tetratricopeptide repeats 1, HGNC:29175) is a protein-coding gene on chromosome 1p36.11, encoding WD and tetratricopeptide repeats protein 1 (Q8N5D0). May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex.

Predicted to enable enzyme inhibitor activity; histone binding activity; and histone deacetylase binding activity. Predicted to be involved in negative regulation of fatty acid biosynthetic process. Predicted to act upstream of or within several processes, including cellular response to insulin stimulus; glucose metabolic process; and negative regulation of transcription by RNA polymerase II. Predicted to be located in nucleoplasm. Predicted to be part of Cul4-RING E3 ubiquitin ligase complex. Predicted to be active in cytoplasm.

Source: NCBI Gene 23038 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 87 total — 1 likely-pathogenic
  • MANE Select transcript: NM_001276252

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:29175
Approved symbolWDTC1
NameWD and tetratricopeptide repeats 1
Location1p36.11
Locus typegene with protein product
StatusApproved
AliasesKIAA1037, ADP, DCAF9
Ensembl geneENSG00000142784
Ensembl biotypeprotein_coding
OMIM619763
Entrez23038

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 16 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000319394, ENST00000361771, ENST00000447062, ENST00000472249, ENST00000491239, ENST00000868293, ENST00000868294, ENST00000868295, ENST00000868296, ENST00000868297, ENST00000868298, ENST00000868299, ENST00000868300, ENST00000868301, ENST00000868302, ENST00000913940, ENST00000913941, ENST00000913942, ENST00000913943

RefSeq mRNA: 3 — MANE Select: NM_001276252 NM_001276252, NM_001410767, NM_015023

CCDS: CCDS296, CCDS60044, CCDS90895

Canonical transcript exons

ENST00000319394 — 16 exons

ExonStartEnd
ENSE000016856462723463227234951
ENSE000034650392729632627296401
ENSE000035109312729402227294116
ENSE000035396182729451427294629
ENSE000035738352729793827298111
ENSE000035765852730618627308636
ENSE000035846152729221527292397
ENSE000036609832730122627301461
ENSE000036712362729704827297156
ENSE000038892562730500127305193
ENSE000038897852726095627261102
ENSE000038929212728333827283449
ENSE000038930532728223927282285
ENSE000038931822728767427287861
ENSE000038942622726315227263235
ENSE000038948892730362127303795

Expression profiles

Bgee: expression breadth ubiquitous, 281 present calls, max score 94.76.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 19.4334 / max 279.1184, expressed in 1812 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
16927.38901761
16935.46191616
16945.27301618
16951.0919705
16910.217667

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
hindlimb stylopod muscleUBERON:000425294.76gold quality
gastrocnemiusUBERON:000138894.65gold quality
muscle of legUBERON:000138394.14gold quality
pancreatic ductal cellCL:000207993.26gold quality
cardia of stomachUBERON:000116293.12gold quality
apex of heartUBERON:000209892.79gold quality
muscle organUBERON:000163092.69gold quality
granulocyteCL:000009492.42gold quality
heart left ventricleUBERON:000208492.17gold quality
right atrium auricular regionUBERON:000663192.16gold quality
cardiac ventricleUBERON:000208292.02gold quality
left testisUBERON:000453391.95gold quality
right testisUBERON:000453491.80gold quality
nippleUBERON:000203091.78gold quality
cardiac atriumUBERON:000208191.75gold quality
bloodUBERON:000017891.62gold quality
vena cavaUBERON:000408791.47gold quality
prefrontal cortexUBERON:000045191.15gold quality
body of tongueUBERON:001187691.13gold quality
heartUBERON:000094891.00gold quality
lower esophagus muscularis layerUBERON:003583390.98gold quality
lower esophagusUBERON:001347390.96gold quality
tongueUBERON:000172390.90gold quality
pylorusUBERON:000116690.89gold quality
Brodmann (1909) area 10UBERON:001354190.76silver quality
stromal cell of endometriumCL:000225590.75gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451190.70gold quality
superior surface of tongueUBERON:000737190.70gold quality
mucosa of stomachUBERON:000119990.68gold quality
left adrenal gland cortexUBERON:003582590.67gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.29

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPG, NFKB, SSRP1, TFAP2A

miRNA regulators (miRDB)

179 targeting WDTC1, 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-6127100.0066.762188
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-4510100.0066.602050
HSA-MIR-6129100.0066.462080
HSA-MIR-6130100.0066.692012
HSA-MIR-6133100.0066.482064
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-9-5P100.0072.282361
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-8485100.0077.574731
HSA-MIR-4533100.0069.482758
HSA-MIR-3667-3P99.9967.171636
HSA-MIR-807599.9767.20962
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-9-3P99.9670.882068
HSA-MIR-185-3P99.9567.011743
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-497-5P99.9271.832674
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-4731-5P99.8967.232537

Literature-anchored findings (GeneRIF, showing 4)

  • WDTC1 variation may be an important risk factor contributing to obesity in both Puerto Rican and white populations. (PMID:19238144)
  • High adp expression in human adipose tissue is associated with lower adiposity and enhanced glucose utilization. (PMID:23512946)
  • Our results identify a biochemical role for WDTC1 and extend the functional range of the CRL4 complex to the suppression of fat accumulation. (PMID:27113764)
  • The putative oncogenic role of WDTC1 in colorectal cancer. (PMID:35238908)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriowdtc1ENSDARG00000059760
mus_musculusWdtc1ENSMUSG00000037622
rattus_norvegicusWdtc1ENSRNOG00000008377
drosophila_melanogasteradpFBGN0000057
caenorhabditis_elegansadpr-1WBGENE00044440

Paralogs (5): DCAF8 (ENSG00000132716), DCAF5 (ENSG00000139990), DCAF6 (ENSG00000143164), DCAF8L2 (ENSG00000189186), DCAF8L1 (ENSG00000226372)

Protein

Protein identifiers

WD and tetratricopeptide repeats protein 1Q8N5D0 (reviewed: Q8N5D0)

All UniProt accessions (2): Q8N5D0, H0YEI6

UniProt curated annotations — full annotation on UniProt →

Function. May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex.

Pathway. Protein modification; protein ubiquitination.

Isoforms (6)

UniProt IDNamesCanonical?
Q8N5D0-11yes
Q8N5D0-22
Q8N5D0-33
Q8N5D0-44
Q8N5D0-55
Q8N5D0-66

RefSeq proteins (3): NP_001263181, NP_001397696, NP_055838 (=MANE)

Domains & families (InterPro)

IDNameType
IPR001680WD40_rptRepeat
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR015943WD40/YVTN_repeat-like_dom_sfHomologous_superfamily
IPR019734TPR_rptRepeat
IPR036322WD40_repeat_dom_sfHomologous_superfamily
IPR045151DCAF8Family

Pfam: PF00400

UniProt features (19 total): repeat 9, splice variant 3, region of interest 2, modified residue 2, chain 1, sequence conflict 1, helix 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
3I7NX-RAY DIFFRACTION2.8

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N5D0-F182.350.64

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): 353, 511

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8951664Neddylation

MSigDB gene sets: 267 (showing top): GOBP_RESPONSE_TO_NITROGEN_COMPOUND, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, MYOGENIN_Q6, TGCGCANK_UNKNOWN, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GOBP_NEGATIVE_REGULATION_OF_LIPID_METABOLIC_PROCESS, GOBP_GROWTH, GOBP_NEGATIVE_REGULATION_OF_LIPID_BIOSYNTHETIC_PROCESS, AP4_Q6, AP2_Q3, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, GOBP_KETONE_METABOLIC_PROCESS, CAGCTG_AP4_Q5, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS

GO Biological Process (9): negative regulation of transcription by RNA polymerase II (GO:0000122), in utero embryonic development (GO:0001701), glucose metabolic process (GO:0006006), regulation of cell size (GO:0008361), protein ubiquitination (GO:0016567), cellular response to insulin stimulus (GO:0032869), multicellular organism growth (GO:0035264), negative regulation of fatty acid biosynthetic process (GO:0045717), intracellular chemical homeostasis (GO:0055082)

GO Molecular Function (4): enzyme inhibitor activity (GO:0004857), histone binding (GO:0042393), histone deacetylase binding (GO:0042826), protein binding (GO:0005515)

GO Cellular Component (5): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), cytosol (GO:0005829), Cul4-RING E3 ubiquitin ligase complex (GO:0080008), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
negative regulation of DNA-templated transcription1
chordate embryonic development1
hexose metabolic process1
regulation of cellular component size1
protein modification by small protein conjugation1
response to insulin1
cellular response to peptide hormone stimulus1
multicellular organismal process1
developmental growth1
fatty acid biosynthetic process1
regulation of fatty acid biosynthetic process1
negative regulation of fatty acid metabolic process1
negative regulation of lipid biosynthetic process1
cellular homeostasis1
chemical homeostasis1
catalytic activity1
enzyme regulator activity1
molecular function inhibitor activity1
protein binding1
enzyme binding1
binding1
nuclear lumen1
intracellular anatomical structure1
cytoplasm1
cullin-RING ubiquitin ligase complex1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

1002 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
WDTC1DDB1Q16531628
WDTC1MAPTP10636541
WDTC1ZNF70Q9UC06493
WDTC1SYNPO2LQ9H987485
WDTC1PARK7Q99497438
WDTC1ZC3H14Q6PJT7425
WDTC1KANSL1Q7Z3B3424
WDTC1HOOK2Q96ED9411
WDTC1DNASE2O00115410
WDTC1DEFA4P12838409
WDTC1DCAF4Q8WV16409
WDTC1DDB2Q92466404
WDTC1MRTO4Q9UKD2399
WDTC1PLAGL2Q9UPG8398
WDTC1SUMO2P55855390

IntAct

87 interactions, top by confidence:

ABTypeScore
SEPTIN3SEPTIN6psi-mi:“MI:0914”(association)0.800
CUL4BCOPS2psi-mi:“MI:0914”(association)0.790
COPS6RHOBTB1psi-mi:“MI:0914”(association)0.730
CCT2TXNDC9psi-mi:“MI:0914”(association)0.730
CUL4ACOPS2psi-mi:“MI:0914”(association)0.640
BCKDKCETN3psi-mi:“MI:0914”(association)0.640
CCT3TXNDC9psi-mi:“MI:0914”(association)0.640
ARL4CRGS12psi-mi:“MI:0914”(association)0.640
BOD1WDTC1psi-mi:“MI:0915”(physical association)0.620
PNOCCETN3psi-mi:“MI:0914”(association)0.530
TRMT10BMRPS14psi-mi:“MI:0914”(association)0.530
ARHGAP44VPS26Apsi-mi:“MI:0914”(association)0.530
WDTC1TCP1psi-mi:“MI:0914”(association)0.530
SLC25A22DNLZpsi-mi:“MI:0914”(association)0.530
BOD1PLXDC2psi-mi:“MI:0914”(association)0.530
CCT7PEX7psi-mi:“MI:0914”(association)0.530
MRPS11MRPS14psi-mi:“MI:0914”(association)0.530
PNOCNUP155psi-mi:“MI:0914”(association)0.530
GALNSFBXO21psi-mi:“MI:0914”(association)0.530
APBA3CLSTN1psi-mi:“MI:0914”(association)0.530
GALNSCLGNpsi-mi:“MI:0914”(association)0.530

BioGRID (409): DDB1 (Affinity Capture-Western), CUL4A (Affinity Capture-Western), WDTC1 (Affinity Capture-MS), WDTC1 (Affinity Capture-MS), WDTC1 (Affinity Capture-MS), WDTC1 (Affinity Capture-MS), WDTC1 (Affinity Capture-MS), WDTC1 (Affinity Capture-Western), WDTC1 (Affinity Capture-Western), DDB1 (Affinity Capture-Western), CUL4A (Affinity Capture-Western), CUL4B (Affinity Capture-Western), RBX1 (Affinity Capture-Western), STXBP4 (Affinity Capture-MS), CUL4A (Affinity Capture-MS)

ESM2 similar proteins: A0A2R8QP51, E9PYK3, E9Q4Z2, G1SPE9, O00763, O15228, O23617, P13676, P13798, P19205, P25154, P35574, P80227, P83006, P98192, Q10MJ1, Q2PQH8, Q338C0, Q496Z0, Q5EBA1, Q5IH13, Q5IH14, Q5R5S1, Q5U5V2, Q5ZIB9, Q641Y5, Q6V1X1, Q6YXW6, Q80YA7, Q80YD1, Q80ZK9, Q86TI2, Q8BVG4, Q8C0P5, Q8C5P5, Q8IYB8, Q8K4M9, Q8N5D0, Q8R146, Q8VZF3

Diamond homologs: A4K2V0, A6HD62, A6ZRW3, D7REX8, F1RBN2, F4IRM4, F4JTI1, F4K487, F4KCL7, O13754, O14217, O16259, O35814, O48802, O54981, O94826, O95801, P07213, P23231, P25638, P31948, P33313, P38825, P53041, P53042, Q07617, Q12118, Q13451, Q15785, Q32PZ3, Q3KRD5, Q3ZBR5, Q43207, Q4R8N7, Q5EA11, Q5PPS5, Q5R8D8, Q5RAP0, Q5U2X2, Q5VJS5

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 108 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
Association of TriC/CCT with target proteins during biosynthesis519.3×6e-04
DNA Damage Recognition in GG-NER518.8×6e-04
Formation of TC-NER Pre-Incision Complex513.9×1e-03
Neddylation95.6×1e-03

GO biological processes:

GO termPartnersFoldFDR
binding of sperm to zona pellucida625.3×5e-05
protein folding88.3×9e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic1
Uncertain significance68
Likely benign0
Benign5

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4813977NM_001276252.2(WDTC1):c.1099C>T (p.Gln367Ter)Likely pathogenic

SpliceAI

3200 predictions. Top by Δscore:

VariantEffectΔscore
1:27263148:CTAG:Cacceptor_loss1.0000
1:27263149:TAG:Tacceptor_loss1.0000
1:27263150:A:ACacceptor_loss1.0000
1:27263151:GGA:Gacceptor_gain1.0000
1:27263151:GGAGC:Gacceptor_gain1.0000
1:27263235:GGT:Gdonor_loss1.0000
1:27263236:G:Cdonor_loss1.0000
1:27263237:T:Gdonor_loss1.0000
1:27282281:GGAGA:Gdonor_gain1.0000
1:27282282:GAGA:Gdonor_gain1.0000
1:27282282:GAGAG:Gdonor_gain1.0000
1:27282283:A:Tdonor_gain1.0000
1:27282284:GA:Gdonor_gain1.0000
1:27282286:G:GGdonor_gain1.0000
1:27283334:TCAG:Tacceptor_loss1.0000
1:27283335:CA:Cacceptor_loss1.0000
1:27283336:A:AGacceptor_gain1.0000
1:27283336:A:Cacceptor_loss1.0000
1:27283336:AGCTT:Aacceptor_gain1.0000
1:27283337:G:GGacceptor_gain1.0000
1:27283337:GC:Gacceptor_gain1.0000
1:27283337:GCT:Gacceptor_gain1.0000
1:27283337:GCTT:Gacceptor_gain1.0000
1:27283337:GCTTG:Gacceptor_gain1.0000
1:27287671:T:Gacceptor_gain1.0000
1:27287672:A:AGacceptor_gain1.0000
1:27287673:G:GGacceptor_gain1.0000
1:27287673:GTTC:Gacceptor_gain1.0000
1:27292213:A:AGacceptor_gain1.0000
1:27292214:G:GAacceptor_gain1.0000

AlphaMissense

4486 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:27263231:T:CL43P1.000
1:27282244:C:AH46Q1.000
1:27282244:C:GH46Q1.000
1:27282249:G:AG48E1.000
1:27282251:T:AC49S1.000
1:27282251:T:CC49R1.000
1:27282252:G:AC49Y1.000
1:27282252:G:CC49S1.000
1:27282254:G:TV50F1.000
1:27282255:T:AV50D1.000
1:27282257:A:GN51D1.000
1:27282259:C:AN51K1.000
1:27282259:C:GN51K1.000
1:27282264:T:CL53P1.000
1:27282269:T:AW55R1.000
1:27282269:T:CW55R1.000
1:27282270:G:CW55S1.000
1:27282271:G:CW55C1.000
1:27282271:G:TW55C1.000
1:27283343:T:CL62P1.000
1:27283346:C:AA63D1.000
1:27283348:T:CS64P1.000
1:27283349:C:AS64Y1.000
1:27283349:C:TS64F1.000
1:27283352:G:AG65D1.000
1:27283354:T:CS66P1.000
1:27283355:C:TS66F1.000
1:27283357:G:CD67H1.000
1:27283357:G:TD67Y1.000
1:27283358:A:CD67A1.000

dbSNP variants (sampled 300 via entrez): RS1000009528 (1:27235437 T>TCC), RS1000013999 (1:27276075 A>G), RS1000023631 (1:27304254 C>T), RS1000082223 (1:27261504 T>C), RS1000087532 (1:27283849 A>C), RS1000174509 (1:27297284 A>T), RS1000204775 (1:27305723 G>A), RS1000267951 (1:27261068 A>G), RS1000285456 (1:27255602 T>C), RS1000388349 (1:27248199 C>G), RS1000429174 (1:27241274 T>C), RS1000441129 (1:27299192 T>C), RS1000504379 (1:27304585 C>T), RS1000535320 (1:27304265 T>C), RS1000567870 (1:27254275 C>T)

Disease associations

OMIM: gene MIM:619763 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteincreases expression, affects cotreatment, decreases expression, increases abundance3
Arsenicaffects cotreatment, decreases expression, increases abundance, increases expression2
Rotenonedecreases expression2
FR900359increases phosphorylation1
methylmercuric chloridedecreases expression1
triphenyl phosphateaffects expression1
bisphenol Aincreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
azoxystrobindecreases expression1
CGP 52608affects binding, increases reaction1
deguelindecreases expression1
pyrimidifendecreases expression1
thifluzamidedecreases expression1
pyrachlostrobindecreases expression1
picoxystrobindecreases expression1
Zoledronic Acidincreases expression1
Fulvestrantincreases methylation1
Acetaminophenincreases expression1
Antimycin Adecreases expression1
Benzo(a)pyreneincreases methylation1
Diazinonincreases methylation1
Methapyrileneincreases methylation1
Tetrachlorodibenzodioxinaffects expression1
Urethaneincreases expression1
Valproic Acidaffects expression1
Aflatoxin B1increases methylation1
Cadmium Chloridedecreases expression1
Acrylamidedecreases 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.