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Aliases for HOXD12 Gene

Aliases for HOXD12 Gene

  • Homeobox D12 2 3 5
  • Homeobox Protein Hox-4H 3 4
  • Homeo Box D12 2 3
  • HOX4H 3 4
  • Hox-4.7, Mouse, Homolog Of 3
  • Homeobox Protein Hox-D12 3

External Ids for HOXD12 Gene

Previous HGNC Symbols for HOXD12 Gene

  • HOX4H

Previous GeneCards Identifiers for HOXD12 Gene

  • GC02P175017
  • GC02P175625
  • GC02P176930
  • GC02P177168
  • GC02P177169
  • GC02P176790
  • GC02P176672
  • GC02P168842

Summaries for HOXD12 Gene

Entrez Gene Summary for HOXD12 Gene

  • 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. [provided by RefSeq, Jul 2008]

GeneCards Summary for HOXD12 Gene

HOXD12 (Homeobox D12) is a Protein Coding gene. Diseases associated with HOXD12 include Syndactyly, Type V and Brachydactyly-Syndactyly Syndrome. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HOXC12.

UniProtKB/Swiss-Prot for HOXD12 Gene

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

Gene Wiki entry for HOXD12 Gene

Additional gene information for HOXD12 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HOXD12 Gene

Genomics for HOXD12 Gene

GeneHancer (GH) Regulatory Elements for HOXD12 Gene

Promoters and enhancers for HOXD12 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J176096 Enhancer 0.9 ENCODE 650.7 -1.1 -1140 1.8 ATF1 FOXA2 SIN3A ZNF48 ZNF766 GLIS2 ZNF213 ZNF143 ATF7 NFKBIZ HOXD12 HAGLROS LNPK HOXD13
GH02J176099 Promoter 0.6 EPDnew 650.7 +1.3 1263 0.1 EZH2 GC02P176100 HOXD12 HOXD11
GH02J176172 Promoter/Enhancer 1 EPDnew ENCODE 10.8 +73.4 73357 0.2 USF1 SUZ12 CTBP2 USF2 EZH2 HOXD3 HOXD-AS2 HOXD10 HOXD11 HOXD8 HOXD12 HOXD9 HOXD13 ENSG00000272729 HAGLROS
GH02J176171 Promoter/Enhancer 1 EPDnew ENCODE 10.8 +72.9 72938 0.2 SP1 ZNF143 SIN3A CTBP2 EZH2 HOXD3 HAGLROS HOXD-AS2 HOXD10 HOXD11 HOXD8 HOXD12 HOXD9 HOXD13 ENSG00000272729
GH02J176073 Enhancer 0.8 UCNEbase 11.3 -24.8 -24802 0.5 PKNOX1 HLF ZBTB8A FOXA1 ZNF664 OSR2 PRDM6 EZH2 HOXD11 HOXD12 HOXD10 HOXD1 HAGLR LNPK EVX2 GC02M176020
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HOXD12 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the HOXD12 gene promoter:
  • TBP
  • PPAR-gamma1
  • PPAR-gamma2
  • c-Ets-1
  • E2F
  • E2F-2

Genomic Locations for HOXD12 Gene

Genomic Locations for HOXD12 Gene
5,258 bases
Plus strand
1,951 bases
Plus strand

Genomic View for HOXD12 Gene

Genes around HOXD12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HOXD12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HOXD12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HOXD12 Gene

Proteins for HOXD12 Gene

  • Protein details for HOXD12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein Hox-D12
    Protein Accession:
    Secondary Accessions:
    • B5MCP0
    • Q0VAD7
    • Q0VAD8
    • Q9NS03

    Protein attributes for HOXD12 Gene

    270 amino acids
    Molecular mass:
    29031 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for HOXD12 Gene


neXtProt entry for HOXD12 Gene

Post-translational modifications for HOXD12 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for HOXD12 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HOXD12 Gene

Domains & Families for HOXD12 Gene

Gene Families for HOXD12 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Transcription factors

Suggested Antigen Peptide Sequences for HOXD12 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the Abd-B homeobox family.
  • Belongs to the Abd-B homeobox family.
genes like me logo Genes that share domains with HOXD12: view

Function for HOXD12 Gene

Molecular function for HOXD12 Gene

UniProtKB/Swiss-Prot 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.
GENATLAS Biochemistry:
homeo box D12(4H),homologous to mouse Hox-4.7,interacting with HOD13 during mouse limb development

Phenotypes From GWAS Catalog for HOXD12 Gene

Gene Ontology (GO) - Molecular Function for HOXD12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding NAS 19274049
GO:0003677 DNA binding IEA --
GO:0005515 protein binding IPI 25416956
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HOXD12: view
genes like me logo Genes that share phenotypes with HOXD12: view

Animal Models for HOXD12 Gene

MGI Knock Outs for HOXD12:

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HOXD12 Gene

Localization for HOXD12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HOXD12 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HOXD12 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for HOXD12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with HOXD12: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HOXD12 Gene

Pathways & Interactions for HOXD12 Gene

SuperPathways for HOXD12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for HOXD12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0006357 regulation of transcription by RNA polymerase II IEA --
GO:0007275 multicellular organism development IEA --
genes like me logo Genes that share ontologies with HOXD12: view

No data available for Pathways by source and SIGNOR curated interactions for HOXD12 Gene

Drugs & Compounds for HOXD12 Gene

No Compound Related Data Available

Transcripts for HOXD12 Gene

mRNA/cDNA for HOXD12 Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(3) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HOXD12 Gene

Homeobox D12:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HOXD12 Gene

No ASD Table

Relevant External Links for HOXD12 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HOXD12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HOXD12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HOXD12 Gene

This gene is overexpressed in Vagina (x20.8), Colon - Sigmoid (x12.0), Cervix - Ectocervix (x8.0), and Prostate (x7.1).

NURSA nuclear receptor signaling pathways regulating expression of HOXD12 Gene:


SOURCE GeneReport for Unigene cluster for HOXD12 Gene:

genes like me logo Genes that share expression patterns with HOXD12: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for HOXD12 Gene

Orthologs for HOXD12 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HOXD12 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia HOXD12 34 33
  • 99.14 (n)
(Bos Taurus)
Mammalia HOXD12 34 33
  • 88.72 (n)
(Canis familiaris)
Mammalia HOXD12 34 33
  • 88.27 (n)
(Mus musculus)
Mammalia Hoxd12 16 34 33
  • 84.58 (n)
(Rattus norvegicus)
Mammalia Hoxd12 33
  • 84.2 (n)
(Monodelphis domestica)
Mammalia HOXD12 34
  • 77 (a)
(Ornithorhynchus anatinus)
Mammalia HOXD12 34
  • 70 (a)
(Gallus gallus)
Aves HOXD12 34 33
  • 65.29 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 85 (a)
(Danio rerio)
Actinopterygii hoxd12a 34 33
  • 54.65 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 15 (a)
Species where no ortholog for HOXD12 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HOXD12 Gene

Gene Tree for HOXD12 (if available)
Gene Tree for HOXD12 (if available)
Evolutionary constrained regions (ECRs) for HOXD12: view image

Paralogs for HOXD12 Gene

(8) SIMAP similar genes for HOXD12 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with HOXD12: view

Variants for HOXD12 Gene

Sequence variations from dbSNP and Humsavar for HOXD12 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000189431 -- 176,099,216(+) G/A upstream_transcript_variant
rs1000488319 -- 176,099,403(+) T/A upstream_transcript_variant
rs1000891192 -- 176,100,766(+) C/A downstream_transcript_variant
rs1001276988 -- 176,098,474(+) G/A upstream_transcript_variant
rs1002252417 -- 176,100,104(+) T/G coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for HOXD12 Gene

Variant ID Type Subtype PubMed ID
dgv676n67 CNV gain 20364138
dgv7173n54 CNV loss 21841781
nsv517968 CNV loss 19592680
nsv520227 CNV loss 19592680
nsv524250 CNV loss 19592680
nsv527187 CNV loss 19592680
nsv583673 CNV loss 21841781

Variation tolerance for HOXD12 Gene

Residual Variation Intolerance Score: 86.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.98; 68.20% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HOXD12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HOXD12 Gene

Disorders for HOXD12 Gene

MalaCards: The human disease database

(2) MalaCards diseases for HOXD12 Gene - From: GeneCards

Disorder Aliases PubMed IDs
syndactyly, type v
  • sdty5
brachydactyly-syndactyly syndrome
  • bdsd
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for HOXD12

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with HOXD12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HOXD12 Gene

Publications for HOXD12 Gene

  1. EVX2, a human homeobox gene homologous to the even-skipped segmentation gene, is localized at the 5' end of HOX4 locus on chromosome 2. (PMID: 1675198) D'Esposito M … Boncinelli E (Genomics 1991) 2 3 4 58
  2. Study of HOXD genes in autism particularly regarding the ratio of second to fourth digit length. (PMID: 19540081) Sugie Y … Osawa J (Brain & development 2010) 3 44 58
  3. High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men. (PMID: 19453261) Yerges LM … MrOS Research Group (Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research 2009) 3 44 58
  4. Altered transmission of HOX and apoptotic SNPs identify a potential common pathway for clubfoot. (PMID: 19938081) Ester AR … Hecht JT (American journal of medical genetics. Part A 2009) 3 44 58
  5. [Analysis of association between 5' HOXD gene and idiopathic congenital talipes equinovarus]. (PMID: 16331564) Wang LL … Sun KL (Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics 2005) 3 44 58

Products for HOXD12 Gene

Sources for HOXD12 Gene

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