HOXD8

gene
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Summary

HOXD8 (homeobox D8, HGNC:5139) is a protein-coding gene on chromosome 2q31.1, encoding Homeobox protein Hox-D8 (P13378). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5’ end of this cluster have been associated with severe limb and genital abnormalities. In addition to effects during embryogenesis, this particular gene may also play a role in adult urogenital tract function. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 3234 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 70 total
  • MANE Select transcript: NM_019558

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5139
Approved symbolHOXD8
Namehomeobox D8
Location2q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000175879
Ensembl biotypeprotein_coding
OMIM142985
Entrez3234

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000313173, ENST00000429017, ENST00000450510, ENST00000544999

RefSeq mRNA: 3 — MANE Select: NM_019558 NM_001199746, NM_001199747, NM_019558

CCDS: CCDS2268, CCDS56148, CCDS56149

Canonical transcript exons

ENST00000313173 — 2 exons

ExonStartEnd
ENSE00001270639176131317176132695
ENSE00001270651176129705176130943

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 96.52.

FANTOM5 (CAGE): breadth broad, TPM avg 2.8038 / max 63.8744, expressed in 680 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter IDTPM avgSamples expressed
238482.0610622
238490.3550178
238520.173293
238500.068817
2024820.060017
238510.059015
238460.01323
238470.00772
238450.00602

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
germinal epithelium of ovaryUBERON:000130496.52gold quality
calcaneal tendonUBERON:000370194.48gold quality
adult mammalian kidneyUBERON:000008294.16gold quality
kidneyUBERON:000211392.91gold quality
metanephros cortexUBERON:001053392.78gold quality
corpus epididymisUBERON:000435991.59gold quality
renal medullaUBERON:000036291.44gold quality
kidney epitheliumUBERON:000481991.02gold quality
cortex of kidneyUBERON:000122590.38gold quality
deltoidUBERON:000147689.61gold quality
metanephrosUBERON:000008189.15gold quality
secondary oocyteCL:000065588.79gold quality
tendonUBERON:000004388.70gold quality
body of uterusUBERON:000985387.99gold quality
hindlimb stylopod muscleUBERON:000425287.87gold quality
oviduct epitheliumUBERON:000480487.72gold quality
left ovaryUBERON:000211987.40gold quality
ovaryUBERON:000099287.27gold quality
right ovaryUBERON:000211887.19gold quality
adrenal tissueUBERON:001830386.25gold quality
caput epididymisUBERON:000435884.74gold quality
left adrenal gland cortexUBERON:003582584.70gold quality
left adrenal glandUBERON:000123484.68gold quality
smooth muscle tissueUBERON:000113584.63gold quality
right adrenal gland cortexUBERON:003582784.33gold quality
right testisUBERON:000453484.27gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.22gold quality
right adrenal glandUBERON:000123384.22gold quality
fallopian tubeUBERON:000388984.21gold quality
adrenal glandUBERON:000236983.84gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-10yes20.41
E-ANND-3yes7.85

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

5 targets.

TargetRegulation
ANGPT2Activation
CDKN2A
KDM1A
PROX1Activation
TTF1

JASPAR motifs

MotifNameFamily
MA0910.2HOXD8HOX
MA0910.3HOXD8HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): PROX1

miRNA regulators (miRDB)

73 targeting HOXD8, 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-5692A100.0074.406850
HSA-MIR-340-5P100.0072.504437
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-477599.9875.006394
HSA-MIR-569699.9872.364487
HSA-MIR-60799.9773.625593
HSA-MIR-302E99.9670.742669
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-590-3P99.9674.346478
HSA-MIR-6835-3P99.9370.492904
HSA-MIR-367199.9073.043897
HSA-MIR-302A-3P99.8971.231777
HSA-MIR-302B-3P99.8971.231777
HSA-MIR-302C-3P99.8971.201778
HSA-MIR-302D-3P99.8971.251777
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-548BB-3P99.8670.584354
HSA-MIR-369-3P99.8570.522264
HSA-MIR-548AC99.8470.774351
HSA-MIR-548H-3P99.8470.804349
HSA-MIR-548Z99.8470.804349
HSA-MIR-576-5P99.8470.462582
HSA-MIR-373-3P99.8470.681668
HSA-MIR-520E-3P99.8470.551698

Literature-anchored findings (GeneRIF, showing 10)

  • Prox1 and HoxD8 play important roles in the maturation and maintenance of lymphatic vessels. (PMID:19825936)
  • microRNA-520a-3p inhibits proliferation and cancer stem cell phenotype by targeting HOXD8 in non small cell lung cancer cells and restoration of microRNA-520a-3p might be a therapeutic strategy to reverse gefitinib resistance. (PMID:27748920)
  • HOXD8 exerts a tumor-suppressing role in colorectal cancer as an apoptotic inducer (PMID:28457970)
  • Taken together, these results suggest that HOXD8 is potentially associated with both cisplatin resistance and metastasis in advanced ovarian cancer. (PMID:30194340)
  • Two transcription factors, HOXD8 and Lhx3, predicted to regulate the expression of lncRNAs, were also selected. Using RNA interference technology, HOXD8 and Lhx3 were found to positively regulate DIAPH2-AS1 and RP11-445K13.2 in HTR-8/SVneo cells (PMID:30626726)
  • verified that HOXD8 was a target of miR-5692a via online prediction database and dual luciferase reporter assay (PMID:30941968)
  • LINC01106 post-transcriptionally regulates ELK3 and HOXD8 to promote bladder cancer progression. (PMID:33311496)
  • HOXD8 inhibits the proliferation and migration of triple-negative breast cancer cells and induces apoptosis in them through regulation of AKT/mTOR pathway. (PMID:34454307)
  • HOXD8 hypermethylation as a fully sensitive and specific biomarker for biliary tract cancer detectable in tissue and bile samples. (PMID:35177798)
  • CircTMEM59 Serves as miR-410-3p Sponge to Inhibit the Proliferation and Metastasis of Colorectal Cancer by Regulating HOXD8. (PMID:35426617)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusHoxd8ENSMUSG00000027102
rattus_norvegicusHoxd8ENSRNOG00000071108

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-D8P13378 (reviewed: P13378)

Alternative names: Homeobox protein Hox-4E, Homeobox protein Hox-5.4

All UniProt accessions (3): A0A0A0MSX5, A0A0A0MTF4, P13378

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Subcellular location. Nucleus.

Similarity. Belongs to the Antp homeobox family.

Isoforms (3)

UniProt IDNamesCanonical?
P13378-11yes
P13378-22
P13378-33

RefSeq proteins (3): NP_001186675, NP_001186676, NP_062458* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR001827Homeobox_Antennapedia_CSConserved_site
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR020479HD_metazoaDomain
IPR050948Antp_homeobox_TFFamily

Pfam: PF00046

UniProt features (13 total): splice variant 3, region of interest 3, compositionally biased region 3, sequence conflict 2, chain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P13378-F163.280.22

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 144 (showing top): ATF_B, WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, BENPORATH_ES_WITH_H3K27ME3, GOBP_AXIS_SPECIFICATION, WWTAAGGC_UNKNOWN, TSENG_IRS1_TARGETS_UP, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_AXIS_SPECIFICATION, NKX25_02, TGCACTT_MIR519C_MIR519B_MIR519A, AREB6_01, CREBP1_Q2, NKX61_01, PAX8_B, GOBP_ANIMAL_ORGAN_MORPHOGENESIS

GO Biological Process (7): negative regulation of transcription by RNA polymerase II (GO:0000122), regulation of transcription by RNA polymerase II (GO:0006357), anterior/posterior axis specification, embryo (GO:0008595), positive regulation of transcription by RNA polymerase II (GO:0045944), skeletal system morphogenesis (GO:0048705), regulation of DNA-templated transcription (GO:0006355), anterior/posterior pattern specification (GO:0009952)

GO Molecular Function (7): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
regulation of transcription by RNA polymerase II3
transcription by RNA polymerase II3
regulation of DNA-templated transcription2
transcription cis-regulatory region binding2
RNA polymerase II transcription regulatory region sequence-specific DNA binding2
negative regulation of DNA-templated transcription1
embryonic axis specification1
tripartite regional subdivision1
anterior/posterior axis specification1
positive regulation of DNA-templated transcription1
skeletal system development1
animal organ morphogenesis1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
regionalization1
chromatin1
DNA-binding transcription factor activity1
DNA-binding transcription factor activity, RNA polymerase II-specific1
DNA-binding transcription activator activity1
positive regulation of transcription by RNA polymerase II1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
transcription regulator activity1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

816 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HOXD8HOXB5P09067545
HOXD8CRIP3Q6Q6R5538
HOXD8HOXA9P31269523
HOXD8HOXA3O43365510
HOXD8HOXB4P17483489
HOXD8SUZ12Q15022468
HOXD8HOXA6P31267452
HOXD8HOXC9P31274409
HOXD8ISL1P20663403
HOXD8TBX15Q96SF7399
HOXD8COL2A1P02458385
HOXD8HOXC4P09017383
HOXD8EVX2Q03828367
HOXD8HOXD1Q9GZZ0363
HOXD8HOXD13P35453357

IntAct

21 interactions, top by confidence:

ABTypeScore
HOXD8BAIAP2psi-mi:“MI:0915”(physical association)0.560
HOXD8LDLRAP1psi-mi:“MI:0915”(physical association)0.560
NCK2HOXD8psi-mi:“MI:0915”(physical association)0.560
IFNA10HOXD8psi-mi:“MI:0915”(physical association)0.370
ANXA7HOXD8psi-mi:“MI:0915”(physical association)0.370
HOXD8CDKN1Apsi-mi:“MI:0915”(physical association)0.370
PFDN1HOXD8psi-mi:“MI:0915”(physical association)0.370
HOXD8RCC1psi-mi:“MI:0915”(physical association)0.370
LPXNpsi-mi:“MI:0915”(physical association)0.370
HOXD8psi-mi:“MI:0915”(physical association)0.370
HOXD8psi-mi:“MI:0915”(physical association)0.370
LDLRAP1HOXD8psi-mi:“MI:0915”(physical association)0.000
BAIAP2HOXD8psi-mi:“MI:0915”(physical association)0.000
NCK2HOXD8psi-mi:“MI:0915”(physical association)0.000

BioGRID (14): HOXD8 (Two-hybrid), HOXD8 (Two-hybrid), HOXD8 (Two-hybrid), HOXD8 (Reconstituted Complex), HOXD8 (Proximity Label-MS), HOXD8 (Proximity Label-MS), HOXD8 (Proximity Label-MS), HOXD8 (Proximity Label-MS), HOXD8 (Proximity Label-MS), HOXD8 (Two-hybrid), HOXD8 (Two-hybrid), HOXD8 (Two-hybrid), HOXD8 (Two-hybrid), HOXD8 (Two-hybrid)

ESM2 similar proteins: A1YER7, A1YF08, A1YFD8, A1YFY3, A1YG01, A1YG85, A2D4P8, A2D4R4, A2D5I1, A2D649, A2T6H5, A2T6X6, A2T6Z0, A2T748, A2T756, A2T7H5, A2T7J2, P06798, P09016, P09017, P09023, P09024, P10284, P10628, P13378, P14653, P17277, P17483, P17509, P18111, P18864, P23463, P23813, P31259, P31275, P31276, P31277, P31310, P47902, P50207

Diamond homologs: A1YER7, A1YFA5, A1YFD8, A1YFY3, A1YGK7, A2D4P8, A2D5I1, A2D5K9, A2D5Y4, A2T6X6, A2T748, A2T7F3, O42504, O57374, P02830, P02832, P02833, P04476, P09013, P09014, P09016, P09019, P09021, P09023, P09024, P09025, P09067, P09071, P09074, P09077, P09079, P09080, P09092, P09629, P09630, P09632, P09634, P09636, P10284, P10628

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

208 predictions. Top by Δscore:

VariantEffectΔscore
2:176131311:A:AGacceptor_gain0.9800
2:176131316:GCA:Gacceptor_gain0.9700
2:176131315:A:AGacceptor_gain0.9500
2:176131316:G:GGacceptor_gain0.9500
2:176131305:T:Aacceptor_gain0.9400
2:176130869:A:AGdonor_gain0.9300
2:176131316:GC:Gacceptor_gain0.9300
2:176131312:A:Gacceptor_gain0.9100
2:176131312:ATCAG:Aacceptor_loss0.9000
2:176131313:TCAGC:Tacceptor_loss0.9000
2:176131316:GCAG:Gacceptor_loss0.9000
2:176131318:A:AGacceptor_gain0.8700
2:176131319:G:GGacceptor_gain0.8700
2:176131316:GCAGC:Gacceptor_gain0.8300
2:176131317:CAGCT:Cacceptor_loss0.8300
2:176131318:AGCTC:Aacceptor_loss0.8300
2:176131319:G:GTacceptor_loss0.8300
2:176129788:C:Adonor_gain0.8200
2:176131319:GCTC:Gacceptor_gain0.8200
2:176130863:GTG:Gdonor_gain0.8100
2:176130939:ACAAG:Adonor_loss0.8100
2:176130940:CAAG:Cdonor_loss0.8100
2:176130941:AAGGT:Adonor_loss0.8100
2:176130942:AGGT:Adonor_loss0.8100
2:176130943:GGTT:Gdonor_loss0.8100
2:176129787:T:TAdonor_gain0.7900
2:176130862:AGT:Adonor_gain0.7900
2:176131313:T:Gacceptor_gain0.7700
2:176130837:AC:Adonor_gain0.7500
2:176129809:C:Tdonor_gain0.7400

AlphaMissense

1891 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:176130928:T:AW188R1.000
2:176130928:T:CW188R1.000
2:176130932:T:CM189T1.000
2:176131349:T:CY204H1.000
2:176131349:T:GY204D1.000
2:176131350:A:GY204C1.000
2:176131363:A:CQ208H1.000
2:176131363:A:TQ208H1.000
2:176131368:T:CL210P1.000
2:176131374:T:CL212S1.000
2:176131374:T:GL212W1.000
2:176131377:A:TE213V1.000
2:176131378:A:CE213D1.000
2:176131378:A:TE213D1.000
2:176131385:T:CF216L1.000
2:176131386:T:CF216S1.000
2:176131386:T:GF216C1.000
2:176131387:T:AF216L1.000
2:176131387:T:GF216L1.000
2:176131404:T:CL222P1.000
2:176131410:G:TR224M1.000
2:176131420:A:CR227S1.000
2:176131420:A:TR227S1.000
2:176131430:T:CS231P1.000
2:176131446:T:AL236H1.000
2:176131446:T:CL236P1.000
2:176131452:A:TE238V1.000
2:176131459:G:CQ240H1.000
2:176131459:G:TQ240H1.000
2:176131463:A:GK242E1.000

dbSNP variants (sampled 300 via entrez): RS1001383013 (2:176130269 G>C,T), RS1001595837 (2:176132415 C>A), RS1002199988 (2:176130834 G>A), RS1002420999 (2:176129922 T>A,C), RS1003391653 (2:176132997 C>G,T), RS1003439768 (2:176129530 A>C,G), RS1003494706 (2:176129151 A>C), RS1003607288 (2:176129183 A>G), RS1003829582 (2:176128942 C>T), RS1004662749 (2:176128819 T>A,G), RS1004695280 (2:176129050 G>C,T), RS1004757602 (2:176128579 G>C), RS1004780332 (2:176130497 ACGC>A,ACGCCGC,ACGCCGCCGC), RS1004831110 (2:176130684 G>GGCC), RS1005917749 (2:176128660 C>T)

Disease associations

OMIM: gene MIM:142985 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST004292_43Glomerular filtration rate (creatinine)5.000000e-10
GCST006661_148Male-pattern baldness3.000000e-18
GCST007344_32Estimated glomerular filtration rate1.000000e-09
GCST007876_9Estimated glomerular filtration rate1.000000e-14
GCST008058_51Estimated glomerular filtration rate8.000000e-30
GCST008059_136Estimated glomerular filtration rate6.000000e-30
GCST008062_101Blood urea nitrogen levels3.000000e-06
GCST008064_27Chronic kidney disease3.000000e-10
GCST008971_140Urate levels3.000000e-11

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement

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
urushioldecreases expression1
methylselenic acidincreases expression1
ascorbate-2-phosphateincreases expression, affects binding, affects cotreatment1
terbufosincreases methylation1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteaffects methylation1
aflatoxin B2increases methylation1
4-(2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl)benzoic acidincreases expression, affects cotreatment1
brequinardecreases expression1
perfluorooctane sulfonic acidincreases expression1
perfluoro-n-nonanoic acidincreases expression1
Chir 99021affects binding, affects cotreatment, increases expression1
XAV939affects binding, affects cotreatment, increases expression1
3-(4-pyridyl)-1H-indoleaffects cotreatment, increases expression1
Temozolomidedecreases expression1
Arsenic Trioxideincreases expression1
Ascorbic Acidaffects binding, affects cotreatment, increases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Fonofosincreases methylation1
Hydrocortisoneaffects cotreatment, increases expression1
Parathionincreases methylation1
Silicon Dioxidedecreases expression1
Triclosanincreases expression1
Valproic Acidincreases methylation1
Aflatoxin B1decreases methylation1
Asbestos, Crocidolitedecreases methylation1
Asbestos, Amositedecreases methylation1
Antirheumatic Agentsincreases 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.