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Aliases for HMX1 Gene

Aliases for HMX1 Gene

  • H6 Family Homeobox 1 2 3 5
  • Homeobox Protein H6 3 4
  • H6 3 4
  • Homeo Box (H6 Family) 1 2
  • H6 Homeodomain Protein 3
  • Homeobox Protein HMX1 3
  • NKX5-3 3

External Ids for HMX1 Gene

Previous GeneCards Identifiers for HMX1 Gene

  • GC04M021233
  • GC04M9E0039
  • GC00M9M0039
  • GC00M9V0039
  • GC04M9P0039
  • GC04M9R0039
  • GC04M008869

Summaries for HMX1 Gene

Entrez Gene Summary for HMX1 Gene

  • This gene encodes a transcription factor that belongs to the H6 family of homeobox proteins. This protein can bind a 5'-CAAG-3' core DNA sequence, and it is involved in the development of craniofacial structures. Mutations in this gene cause oculoauricular syndrome, a disorder of the eye and external ear. [provided by RefSeq, Oct 2009]

GeneCards Summary for HMX1 Gene

HMX1 (H6 Family Homeobox 1) is a Protein Coding gene. Diseases associated with HMX1 include Oculoauricular Syndrome and Duodenal Gastrinoma. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HMX3.

UniProtKB/Swiss-Prot for HMX1 Gene

  • DNA-binding protein that binds to the 5-CAAG-3 core sequence. May function as a transcriptional repressor. Seems to act as a transcriptional antagonist of NKX2-5. May play an important role in the development of craniofacial structures such as the eye and ear.

Additional gene information for HMX1 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HMX1 Gene

Genomics for HMX1 Gene

GeneHancer (GH) Regulatory Elements for HMX1 Gene

Promoters and enhancers for HMX1 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
GH04I008871 Promoter 0.7 EPDnew 550.8 0.0 -30 0.1 ZFX EZH2 HMX1 PIR48033
GH04I008899 Enhancer 0.4 ENCODE 13 -26.7 -26692 0.8 ZNF341 ZIC2 HMX1 PIR46407 PIR51339
GH04I008898 Enhancer 0.2 ENCODE 13 -27.2 -27248 0.1 HMX1 PIR46407 PIR51339
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around HMX1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for HMX1 Gene

Genomic Locations for HMX1 Gene
25,742 bases
Minus strand

Genomic View for HMX1 Gene

Genes around HMX1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HMX1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HMX1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for HMX1 Gene

Proteins for HMX1 Gene

  • Protein details for HMX1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein HMX1
    Protein Accession:

    Protein attributes for HMX1 Gene

    348 amino acids
    Molecular mass:
    36155 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAF70205.1; Type=Frameshift; Positions=35, 60, 84, 89, 157, 179, 277; Evidence={ECO:0000305};

neXtProt entry for HMX1 Gene

Post-translational modifications for HMX1 Gene

No Post-translational modifications

Other Protein References for HMX1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for HMX1 Gene

Domains & Families for HMX1 Gene

Gene Families for HMX1 Gene

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

Suggested Antigen Peptide Sequences for HMX1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the HMX homeobox family.
  • Belongs to the HMX homeobox family.
genes like me logo Genes that share domains with HMX1: view

Function for HMX1 Gene

Molecular function for HMX1 Gene

GENATLAS Biochemistry:
Drosophila NK-3/NK-1 homolog,homeo domain encoding gene
UniProtKB/Swiss-Prot Function:
DNA-binding protein that binds to the 5-CAAG-3 core sequence. May function as a transcriptional repressor. Seems to act as a transcriptional antagonist of NKX2-5. May play an important role in the development of craniofacial structures such as the eye and ear.

Gene Ontology (GO) - Molecular Function for HMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IEA --
GO:0001227 transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA --
GO:0003677 DNA binding IMP 10206974
GO:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with HMX1: view
genes like me logo Genes that share phenotypes with HMX1: view

Human Phenotype Ontology for HMX1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HMX1 Gene

MGI Knock Outs for HMX1:
  • Hmx1 tm1(KOMP)Vlcg

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for HMX1 Gene

Localization for HMX1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HMX1 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 HMX1 gene
Compartment Confidence
nucleus 5
cytosol 2
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for HMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IC,IEA 10206974
genes like me logo Genes that share ontologies with HMX1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HMX1 Gene

Pathways & Interactions for HMX1 Gene

No Data Available

Interacting Proteins for HMX1 Gene

Gene Ontology (GO) - Biological Process for HMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription by RNA polymerase II IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0045892 negative regulation of transcription, DNA-templated IMP,IEA 10206974
genes like me logo Genes that share ontologies with HMX1: view

No data available for Pathways by source and SIGNOR curated interactions for HMX1 Gene

Drugs & Compounds for HMX1 Gene

No Compound Related Data Available

Transcripts for HMX1 Gene

mRNA/cDNA for HMX1 Gene

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

Unigene Clusters for HMX1 Gene

H6 family homeobox 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for HMX1 Gene

No ASD Table

Relevant External Links for HMX1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for HMX1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HMX1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for HMX1 Gene

This gene is overexpressed in Testis (x5.6), Brain - Putamen (basal ganglia) (x5.5), Brain - Substantia nigra (x5.1), Brain - Hypothalamus (x4.6), Brain - Amygdala (x4.3), and Brain - Hippocampus (x4.1).

Protein differential expression in normal tissues from HIPED for HMX1 Gene

This gene is overexpressed in Bone marrow stromal cell (68.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for HMX1 Gene

Protein tissue co-expression partners for HMX1 Gene

NURSA nuclear receptor signaling pathways regulating expression of HMX1 Gene:


SOURCE GeneReport for Unigene cluster for HMX1 Gene:


Evidence on tissue expression from TISSUES for HMX1 Gene

  • Intestine(2.8)
  • Pancreas(2.8)

Phenotype-based relationships between genes and organs from Gene ORGANizer for HMX1 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • immune
  • nervous
Head and neck:
  • brain
  • cranial nerve
  • eye
  • head
  • peripheral nervous system
genes like me logo Genes that share expression patterns with HMX1: view

No data available for mRNA Expression by UniProt/SwissProt for HMX1 Gene

Orthologs for HMX1 Gene

This gene was present in the common ancestor of animals.

Orthologs for HMX1 Gene

Organism Taxonomy Gene Similarity Type Details
(Canis familiaris)
Mammalia HMX1 33 34
  • 91.88 (n)
(Bos Taurus)
Mammalia HMX1 33 34
  • 88.76 (n)
(Rattus norvegicus)
Mammalia Hmx1 33
  • 83.5 (n)
(Mus musculus)
Mammalia Hmx1 33 16 34
  • 82.53 (n)
(Monodelphis domestica)
Mammalia HMX1 34
  • 65 (a)
(Gallus gallus)
Aves HMX1 34
  • 59 (a)
(Anolis carolinensis)
Reptilia -- 34
  • 79 (a)
-- 34
  • 45 (a)
(Danio rerio)
Actinopterygii LOC100333298 33
  • 69.42 (n)
hmx1 34
  • 41 (a)
fruit fly
(Drosophila melanogaster)
Insecta Hmx 34
  • 20 (a)
(Caenorhabditis elegans)
Secernentea ceh-27 34
  • 22 (a)
Species where no ortholog for HMX1 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)
  • chimpanzee (Pan troglodytes)
  • 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)
  • 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)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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)

Evolution for HMX1 Gene

Gene Tree for HMX1 (if available)
Gene Tree for HMX1 (if available)

Paralogs for HMX1 Gene

(5) SIMAP similar genes for HMX1 Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with HMX1: view

Variants for HMX1 Gene

Sequence variations from dbSNP and Humsavar for HMX1 Gene

SNP ID Clin Chr 04 pos Variation AA Info Type
rs876657398 pathogenic, Oculoauricular syndrome 8,868,090(-) T/G coding_sequence_variant, intron_variant, missense_variant
rs534795074 uncertain-significance, not specified 8,867,947(-) C/G/T coding_sequence_variant, intron_variant, missense_variant
rs1000069281 -- 8,854,761(-) T/C genic_downstream_transcript_variant, intron_variant
rs1000308784 -- 8,850,554(-) G/C genic_downstream_transcript_variant, intron_variant
rs1000336046 -- 8,862,096(-) C/G genic_downstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for HMX1 Gene

Variant ID Type Subtype PubMed ID
nsv949788 CNV deletion 24416366
nsv428437 CNV gain 18775914
nsv1144072 CNV deletion 24896259
nsv1136380 CNV deletion 24896259
nsv1073730 CNV deletion 25765185
nsv1005698 CNV gain 25217958
esv34196 OTHER inversion 12058347
esv2763860 CNV gain+loss 21179565
esv2759222 CNV gain+loss 17122850

Variation tolerance for HMX1 Gene

Gene Damage Index Score: 5.75; 73.37% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HMX1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HMX1 Gene

Disorders for HMX1 Gene

MalaCards: The human disease database

(3) MalaCards diseases for HMX1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
oculoauricular syndrome
  • ocacs
duodenal gastrinoma
  • duodenal g-cell gastrin producing tumor
pancreatic agenesis
  • partial pancreatic agenesis
- elite association - COSMIC cancer census association via MalaCards
Search HMX1 in MalaCards View complete list of genes associated with diseases


  • Oculoauricular syndrome (OCACS) [MIM:612109]: A syndrome characterized by microphthalmia, microcornea, anterior segment dysgenesis, cataract, ocular coloboma, retinal pigment epithelium abnormalities, rod-cone dystrophy, and anomalies of the external ear. {ECO:0000269 PubMed:18423520}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for HMX1

genes like me logo Genes that share disorders with HMX1: view

No data available for Genatlas for HMX1 Gene

Publications for HMX1 Gene

  1. Identification and genetic mapping of a homeobox gene to the 4p16.1 region of human chromosome 4. (PMID: 1360670) Stadler HS … Solursh M (Proceedings of the National Academy of Sciences of the United States of America 1992) 2 3 4 58
  2. Mutation in the human homeobox gene NKX5-3 causes an oculo-auricular syndrome. (PMID: 18423520) Schorderet DF … Munier FL (American journal of human genetics 2008) 3 4 58
  3. Transcriptional antagonism between Hmx1 and Nkx2.5 for a shared DNA-binding site. (PMID: 10206974) Amendt BA … Russo AF (The Journal of biological chemistry 1999) 3 4 58
  4. Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method. (PMID: 21697133) Oshikawa M … Kato S (Investigative ophthalmology & visual science 2011) 3 58
  5. Retinal dystrophy in the oculo-auricular syndrome due to HMX1 mutation. (PMID: 21417677) Vaclavik V … Munier FL (Ophthalmic genetics 2011) 3 58

Products for HMX1 Gene

Sources for HMX1 Gene

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