HOXD12

gene
On this page

Summary

HOXD12 (homeobox D12, HGNC:5135) is a protein-coding gene on chromosome 2q31.1, encoding Homeobox protein Hox-D12 (P35452). 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. The exact role of this gene has not been determined.

Source: NCBI Gene 3238 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): clubfoot (Moderate, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 66 total
  • MANE Select transcript: NM_021193

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5135
Approved symbolHOXD12
Namehomeobox D12
Location2q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000170178
Ensembl biotypeprotein_coding
OMIM142988
Entrez3238

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000404162, ENST00000406506

RefSeq mRNA: 1 — MANE Select: NM_021193 NM_021193

CCDS: CCDS46456

Canonical transcript exons

ENST00000406506 — 2 exons

ExonStartEnd
ENSE00001559421176100522176102489
ENSE00001562720176099795176100375

Expression profiles

Bgee: expression breadth broad, 22 present calls, max score 53.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0413 / max 31.8679, expressed in 10 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
238190.041310

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
vaginaUBERON:000099653.87gold quality
muscle layer of sigmoid colonUBERON:003580553.14gold quality
tendon of biceps brachiiUBERON:000818851.36gold quality
rectumUBERON:000105250.09gold quality
ectocervixUBERON:001224949.87gold quality
lower lobe of lungUBERON:000894946.50silver quality
prostate glandUBERON:000236746.34gold quality
uterine cervixUBERON:000000244.78gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451143.37gold quality
sural nerveUBERON:001548843.22gold quality
amniotic fluidUBERON:000017342.95gold quality
secondary oocyteCL:000065542.57gold quality
substantia nigra pars compactaUBERON:000196541.98gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450241.97gold quality
middle temporal gyrusUBERON:000277141.96gold quality
vastus lateralisUBERON:000137941.81gold quality
quadriceps femorisUBERON:000137741.75gold quality
endocervixUBERON:000045841.70silver quality
superficial temporal arteryUBERON:000161441.33gold quality
biceps brachiiUBERON:000150741.14gold quality
palpebral conjunctivaUBERON:000181241.10gold quality
mucosa of paranasal sinusUBERON:000503040.98gold quality
jejunal mucosaUBERON:000039940.59gold quality
epithelium of nasopharynxUBERON:000195140.45gold quality
myocardiumUBERON:000234940.45gold quality
gingival epitheliumUBERON:000194940.43gold quality
mammalian vulvaUBERON:000099740.40gold quality
germinal epithelium of ovaryUBERON:000130440.33gold quality
esophagus squamous epitheliumUBERON:000692040.29gold quality
jejunumUBERON:000211540.18gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.83

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

1 targets.

TargetRegulation
SHH

JASPAR motifs

MotifNameFamily
MA0873.1HOXD12HOX
MA0873.2HOXD12HOX
MA1958.1HOXD12::ELK1HOX::Ets-related
MA1958.2HOXD12::ELK1HOX::Ets-related

JASPAR matrix evidence (PMIDs): PMID:18585359, PMID:24218641

Literature-anchored findings (GeneRIF, showing 4)

  • Data show that HOXD12 are important susceptible genes of idiopathic congenital talipes equinovarus. (PMID:16331564)
  • data show no significant difference in HOXD11, HOXD12 & HOXD13 genotype frequencies between the autism spectrum disorder & healthy controls, but one SNP in promoter region of HOXD11 was observed in only 4 patients with ASD (PMID:19540081)
  • In human embryonic stem cell (hESCs)differentiation, a 1.8kb region between HOXD11 and HOXD12 (D11.12) that is associated with PcG proteins was discovered, it shows alteration in nuclease sensitivity as hESCs differentiate. (PMID:20085705)
  • HOXD12 defines an age-related aggressive subtype of oligodendroglioma. (PMID:39259414)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriohoxd12aENSDARG00000059263
mus_musculusHoxd12ENSMUSG00000001823
rattus_norvegicusHoxd12ENSRNOG00000001587

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), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-D12P35452 (reviewed: P35452)

Alternative names: Homeobox protein Hox-4H

All UniProt accessions (2): P35452, B5MCD3

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 Abd-B homeobox family.

Isoforms (2)

UniProt IDNamesCanonical?
P35452-11yes
P35452-22

RefSeq proteins (1): NP_067016* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR020479HD_metazoaDomain

Pfam: PF00046

UniProt features (10 total): sequence conflict 5, chain 1, DNA-binding region 1, region of interest 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P35452-F165.090.27

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 70 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_UP, BENPORATH_ES_WITH_H3K27ME3, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, PAX8_B, TCF4_Q5, GOBP_APPENDAGE_DEVELOPMENT, MA_MYELOID_DIFFERENTIATION_DN, LEF1_Q6, GOBP_EMBRYO_DEVELOPMENT, PTF1BETA_Q6, LEE_AGING_CEREBELLUM_UP, SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER, GATGKMRGCG_UNKNOWN, GOCC_TRANSCRIPTION_REGULATOR_COMPLEX

GO Biological Process (5): skeletal system development (GO:0001501), pattern specification process (GO:0007389), embryonic digit morphogenesis (GO:0042733), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357)

GO Molecular Function (4): DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), protein binding (GO:0005515)

GO Cellular Component (3): chromatin (GO:0000785), nucleus (GO:0005634), transcription regulator complex (GO:0005667)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
system development1
multicellular organism development1
multicellular organismal process1
embryonic limb morphogenesis1
embryonic morphogenesis1
DNA-templated transcription1
regulation of gene expression1
regulation of RNA biosynthetic process1
regulation of DNA-templated transcription1
transcription by RNA polymerase II1
chromatin1
RNA polymerase II transcription regulatory region sequence-specific DNA binding1
DNA-binding transcription factor activity1
regulation of transcription by RNA polymerase II1
double-stranded DNA binding1
sequence-specific DNA binding1
nucleic acid binding1
binding1
chromosome1
cellular anatomical structure1
intracellular membrane-bounded organelle1
protein-containing complex1

Protein interactions and networks

STRING

750 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HOXD12SHHQ15465759
HOXD12EVX2Q03828583
HOXD12HAND2P61296567
HOXD12HOXD10P28358527
HOXD12HOXD1Q9GZZ0520
HOXD12SUZ12Q15022512
HOXD12ZP2Q05996500
HOXD12SALL1Q9NSC2499
HOXD12GLI3P10071489
HOXD12YY1P25490475
HOXD12SMOC1Q9H4F8438
HOXD12IRX2Q9BZI1429
HOXD12R4GMX3R4GMX3427
HOXD12BMI1P35226426
HOXD12TOX3O15405412

IntAct

6 interactions, top by confidence:

ABTypeScore
HOXD12TRAF1psi-mi:“MI:0915”(physical association)0.560
TRAF1HOXD12psi-mi:“MI:0915”(physical association)0.560
KLRB1HOXD12psi-mi:“MI:0914”(association)0.350
KLRB1ESYT2psi-mi:“MI:0914”(association)0.350

BioGRID (19): TRAF1 (Two-hybrid), HOXD12 (Two-hybrid), HOXD12 (Two-hybrid), HOXD12 (Two-hybrid), HOXD12 (Two-hybrid), HOXD12 (Two-hybrid), HOXD12 (Two-hybrid), POLR1C (Two-hybrid), MKRN3 (Two-hybrid), ACTN3 (Two-hybrid), HOXD12 (Affinity Capture-MS), HOXD12 (Affinity Capture-MS), HOXD12 (Reconstituted Complex), MAFB (Reconstituted Complex), MAFK (Reconstituted Complex)

ESM2 similar proteins: A1YER7, A1YF08, A1YFD8, A1YFY3, A1YG85, A2D4P8, A2D5I1, A2T6X6, A2T756, A2T7H5, A6NCS4, O08934, O14813, O42230, O43763, O70218, O93367, P06798, P09016, P10284, P10628, P13378, P17277, P17483, P18111, P23683, P23813, P31277, P31310, P35452, P42580, P47902, P49640, P50207, P50223, P52945, P52946, P52947, P70118, P82976

Diamond homologs: A1YFT7, A2D5V0, A2D635, A2T6F8, A2T7D1, A2T7H7, G5EFY5, O14627, O42502, O42506, O43248, P02835, P09013, P09067, P09079, P09087, P09631, P09633, P10038, P10179, P17482, P17919, P20615, P23812, P24061, P24341, P24342, P24343, P24344, P28358, P28359, P31257, P31260, P31263, P31268, P31269, P31271, P31272, P31274, P31275

SIGNOR signaling

6 interactions.

AEffectBMechanism
HOXD12“down-regulates activity”MAFFbinding
HOXD12“down-regulates activity”MAFbinding
HOXD12“down-regulates activity”MAFBbinding
HOXD12“down-regulates activity”MAFKbinding
HOXD12“down-regulates activity”MAFGbinding
HOXD12“up-regulates activity”MEIS1binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance63
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

160 predictions. Top by Δscore:

VariantEffectΔscore
2:176100372:GACG:Gdonor_gain0.9900
2:176100372:GACGG:Gdonor_loss0.9900
2:176100376:G:GGdonor_gain0.9900
2:176100377:T:Gdonor_loss0.9900
2:176100093:GC:Gdonor_gain0.9800
2:176100516:TTGCA:Tacceptor_loss0.9800
2:176100517:TGCA:Tacceptor_loss0.9800
2:176100518:GCAG:Gacceptor_loss0.9800
2:176100519:CA:Cacceptor_loss0.9800
2:176100520:A:AGacceptor_gain0.9800
2:176100520:AGG:Aacceptor_loss0.9800
2:176100521:G:GGacceptor_gain0.9800
2:176100515:GTTGC:Gacceptor_loss0.9600
2:176100521:GGC:Gacceptor_gain0.9600
2:176100521:GGCCT:Gacceptor_gain0.9600
2:176100291:G:GTdonor_gain0.9300
2:176100094:C:Gdonor_gain0.9200
2:176100520:AG:Aacceptor_gain0.9200
2:176100521:GG:Gacceptor_gain0.9200
2:176100521:GGCC:Gacceptor_gain0.9200
2:176100514:T:TAacceptor_gain0.8700
2:176100372:G:GTdonor_gain0.8600
2:176100736:G:GTdonor_gain0.8600
2:176100420:G:Tdonor_gain0.8200
2:176100871:T:Aacceptor_gain0.8100
2:176100512:T:Aacceptor_loss0.7800
2:176100406:T:Adonor_gain0.7100
2:176100426:G:Adonor_gain0.6900
2:176100374:CG:Cdonor_gain0.6700
2:176100375:GG:Gdonor_gain0.6700

AlphaMissense

1718 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:176100572:T:CY209H1.000
2:176100572:T:GY209D1.000
2:176100597:T:CL217S1.000
2:176100600:A:TE218V1.000
2:176100608:T:CF221L1.000
2:176100609:T:CF221S1.000
2:176100609:T:GF221C1.000
2:176100610:C:AF221L1.000
2:176100610:C:GF221L1.000
2:176100623:T:CF226L1.000
2:176100624:T:CF226S1.000
2:176100624:T:GF226C1.000
2:176100625:C:AF226L1.000
2:176100625:C:GF226L1.000
2:176100641:C:AR232S1.000
2:176100669:T:AL241H1.000
2:176100669:T:CL241P1.000
2:176100684:T:AV246D1.000
2:176100686:A:GK247E1.000
2:176100688:A:CK247N1.000
2:176100688:A:TK247N1.000
2:176100690:T:CI248T1.000
2:176100690:T:GI248S1.000
2:176100692:T:AW249R1.000
2:176100692:T:CW249R1.000
2:176100694:G:CW249C1.000
2:176100694:G:TW249C1.000
2:176100695:T:AF250I1.000
2:176100695:T:CF250L1.000
2:176100695:T:GF250V1.000

dbSNP variants (sampled 300 via entrez): RS1000189431 (2:176099216 G>A), RS1000488319 (2:176099403 T>A), RS1000614106 (2:176102854 G>A,T), RS1000891192 (2:176100766 C>A,G,T), RS1001276988 (2:176098474 G>A,T), RS1001853922 (2:176102220 A>G), RS1002252417 (2:176100104 T>C,G), RS1002850514 (2:176101023 C>G,T), RS1003070856 (2:176101222 G>A), RS1003664342 (2:176098726 A>T), RS1004629278 (2:176100975 A>C), RS1004665704 (2:176100856 C>G,T), RS1004805739 (2:176100045 C>A), RS1005847287 (2:176099029 T>C), RS1006043488 (2:176099941 G>C)

Disease associations

OMIM: gene MIM:142988 | disease phenotypes:

GenCC curated gene-disease

DiseaseClassificationInheritance
clubfootModerateAutosomal dominant

Mondo (1): clubfoot (MONDO:0007342)

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST005748_3Digit length ratio (right hand)6.000000e-09
GCST005749_5Digit length ratio (left hand)6.000000e-07
GCST005749_6Digit length ratio (left hand)1.000000e-07
GCST005750_4Digit length ratio1.000000e-10
GCST006661_148Male-pattern baldness3.000000e-18

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004841digit length ratio

MeSH disease descriptors (1)

DescriptorNameTree numbers
D003025ClubfootC05.330.488.655.063; C05.330.495.681.063; C05.660.585.512.380.813.063; C16.131.621.585.512.500.681.063

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

14 total (human), top 14 by PubMed support.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression2
CGP 52608increases reaction, affects binding1
Resveratrolaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Air Pollutantsincreases expression, increases abundance1
Cadmiumdecreases expression, increases abundance1
Plant Extractsaffects cotreatment, decreases expression1
Aflatoxin B1decreases methylation1
Asbestos, Serpentinedecreases methylation1
Asbestos, Crocidolitedecreases methylation1
Asbestos, Amositedecreases methylation1
Cadmium Chloridedecreases expression, increases abundance1
Okadaic Aciddecreases expression1
Particulate Matterincreases abundance, increases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT04564430PHASE4UNKNOWNClonidine for Tourniquet-related Pain in Children
NCT04766684PHASE4COMPLETEDClubfoot Tenotomy Trial
NCT02815215EARLY_PHASE1UNKNOWNEfficacy Analysis of Minimally Invasive Carroll’s Technique in Treatment of Congenital Idiopathic Clubfoot
NCT00175708Not specifiedCOMPLETEDPedobarographic Assessments of Clubfoot Treated Patients
NCT00474032Not specifiedUNKNOWNUsing Botox to Treat Patients With Idiopathic Clubfoot
NCT00474344Not specifiedCOMPLETEDGenetic Linkage Study of Idiopathic Talipes Equinovarus (ITEV) (Clubfoot)
NCT00475631Not specifiedWITHDRAWNEconomic Evaluation of Clubfoot Treatment: One Centre’s Experience
NCT00607191Not specifiedCOMPLETEDClubfoot DNA Repository
NCT01050088Not specifiedUNKNOWNSucrose Analgesia in Infants Undergoing Casting for Club Foot
NCT01067651Not specifiedCOMPLETEDComparison of Casting Materials for the Treatment of Clubfoot Using the Ponseti Method
NCT01088828Not specifiedCOMPLETEDExploring the Causes of Clubfoot Using Magnetic Resonance Imaging, MRI
NCT01481324Not specifiedCOMPLETEDOutcomes of Compliance With Brace Wear in Clubfoot
NCT02022267Not specifiedCOMPLETEDGait Analysis in Ponseti Clubfoot
NCT02395185Not specifiedCOMPLETEDA Randomized Controlled Trial of Three Non-pharmacologic Analgesic Techniques for Casting of Clubfoot Infants
NCT02815306Not specifiedCOMPLETEDPolyaxial Brace Fixing for the Treatment of Congenital Clubfoot
NCT03249805Not specifiedUNKNOWNMiracleFeet Foot Abduction Brace Sensor Trial
NCT03580746Not specifiedWITHDRAWNComparison of Ponseti Method Versus Older Treatments in Talipes Equinovarus Through Gait Analysis and Clinical Results
NCT03671863Not specifiedCOMPLETEDChildren Born With Club Feet
NCT03749265Not specifiedUNKNOWNRate Of Residual Clubfoot Deformity With Correlation To Absence Of Peroneus Tertius Muscle
NCT03853811Not specifiedTERMINATEDCustomized Orthosis for Children With Clubfoot
NCT03953430Not specifiedCOMPLETEDGait Analysis in Children With Clubfoot Treated With Tibialis Anterior Tendon Transfer
NCT04212663Not specifiedUNKNOWNA Study on the Treatment of Recurrent Clubfoot With the Tendon Release of Musculi Tibialis Posterior
NCT04693065Not specifiedUNKNOWNPronostic Factors of Long Term Outcome in Patients With Clubfoot Treated by the Ponseti Method
NCT04737083Not specifiedUNKNOWNCGH Array in Bilateral Clubfoot
NCT04897100Not specifiedCOMPLETEDOutcome After Needle vs Blade Achilles Tenotomy in Clubfoot
NCT05293743Not specifiedCOMPLETEDNovel Dynamic Foot Abduction Bar for Treatment of Clubfoot
NCT05456737Not specifiedCOMPLETEDFunctional Assessment in Children With Clubfoot
NCT05767762Not specifiedRECRUITINGEvertor Muscle Activity as a Predictor of Achilles Tenotomy in the Management of Idiopathic Varus Equinus Clubfoot
NCT05794334Not specifiedCOMPLETEDLow Dye Taping Technique Versus Robert Debre Method On Foot Posture And Range Of Motion In Children With Club Foot.
NCT05913934Not specifiedUNKNOWNClubfeet and Twins and Gait Analysis
NCT05957627Not specifiedUNKNOWNManagement of Congenital Talipes Equinovarus by Saleem’s Protocol
NCT06033638Not specifiedCOMPLETEDVideo Documented PBS-Score in Children With Clubfoot
NCT06050564Not specifiedCOMPLETEDTherapeutic Recommendations Based on Clinical History and Video Documented PBS-Score
NCT06050746Not specifiedACTIVE_NOT_RECRUITINGPredictive Value of the PBS-score in Children With Clubfoot
NCT06300645Not specifiedUNKNOWNSPLATT to Peroneus Brevis vs TATT to Lateral Cuneiform
NCT06407739Not specifiedCOMPLETEDThree Phase Physical Therapy in Children With Relapsed Club Foot After Ponseti Treatment
NCT06906406Not specifiedRECRUITINGHealth-Related Quality of Life in Children and Adolescents With Clubfoot
NCT07055672Not specifiedACTIVE_NOT_RECRUITINGClinical Effectiveness of the Modified WalkFlex DB Splint in Children With Congenital Talipes Equinovarus (CTEV)
NCT07125794Not specifiedRECRUITINGOriginal Denis Brawn Brace Versus Its Modification for Management of Relapsed Idiopathic Clubfoot Following Ponseti Casting
NCT07154550Not specifiedRECRUITINGComparing Outcomes and Complications Following Mastisol Application for Clubfoot Casting
  • Associated diseases: clubfoot
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): clubfoot