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] See more...

Aliases for HMX1 Gene

Aliases for HMX1 Gene

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

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 Anterior Segment Dysgenesis. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is HMX3.

UniProtKB/Swiss-Prot Summary 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.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HMX1 Gene

Genomics for HMX1 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for HMX1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J008871 Promoter 1.2 EPDnew Ensembl 600.7 -0.1 -62 0.6 PRDM10 ZIC2 ZSCAN4 PATZ1 EZH2 ZNF341 SP2 TARDBP ZNF580 ZBTB26 HMX1 piR-54034 FAM90A26
GH04J008899 Enhancer 0.3 ENCODE 13 -26.7 -26670 0.8 ZIC2 ZNF341 HMX1 piR-52408 piR-32214-509 FAM90A26
GH04J008898 Enhancer 0.2 ENCODE 13 -27.2 -27226 0.1 HMX1 piR-52408 piR-32214-509 FAM90A26
GH04J008858 Enhancer 0.5 Ensembl 0.4 +13.9 13884 0.7 KDM1A EZH2 ZNF316 MAFK HDAC2 ENSG00000258507 LOC105374474 HMX1 CPZ
GH04J008857 Enhancer 0.4 Ensembl 0.4 +14.7 14738 0.2 EZH2 SPI1 CBX8 ENSG00000258507 LOC105374474 HMX1 CPZ
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HMX1 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HMX1

Genomic Locations for HMX1 Gene

Genomic Locations for HMX1 Gene
chr4:8,846,076-8,871,839
(GRCh38/hg38)
Size:
25,764 bases
Orientation:
Minus strand
chr4:8,847,802-8,873,543
(GRCh37/hg19)
Size:
25,742 bases
Orientation:
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:
    Q9NP08-HMX1_HUMAN
    Recommended name:
    Homeobox protein HMX1
    Protein Accession:
    Q9NP08

    Protein attributes for HMX1 Gene

    Size:
    348 amino acids
    Molecular mass:
    36155 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAF70205.1; Type=Frameshift; Evidence={ECO:0000305};

neXtProt entry for HMX1 Gene

Post-translational modifications for HMX1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

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

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

Protein Domains for HMX1 Gene

InterPro:
Blocks:
  • Lambda and other repressor helix-turn-helix signature
ProtoNet:

Suggested Antigen Peptide Sequences for HMX1 Gene

GenScript: Design optimal peptide antigens:
  • Homeobox protein HMX1 (F1T0J4_HUMAN)
  • Homeobox protein H6 (HMX1_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NP08

UniProtKB/Swiss-Prot:

HMX1_HUMAN :
  • Belongs to the HMX homeobox family.
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

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.
GENATLAS Biochemistry:
Drosophila NK-3/NK-1 homolog,homeo domain encoding gene

Phenotypes From GWAS Catalog for HMX1 Gene

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:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 19274049
GO:0001227 DNA-binding transcription repressor activity, RNA polymerase II-specific 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 Hmx1<tm1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMX1

No data available for Enzyme Numbers (IUBMB) , 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

COMPARTMENTS
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
extracellular 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Gene Ontology (GO) - Cellular Components for HMX1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA,IC 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

PathCards logo

SuperPathways 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:0006355 regulation of transcription, DNA-templated IEA --
GO:0007275 multicellular organism development IEA --
GO:0045892 negative regulation of transcription, DNA-templated IEA,IMP 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 :
4 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HMX1

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

No ASD Table

Relevant External Links for HMX1 Gene

GeneLoc Exon Structure for
HMX1

Expression for HMX1 Gene

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



Protein tissue co-expression partners for HMX1 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HMX1

SOURCE GeneReport for Unigene cluster for HMX1 Gene:

Hs.104134

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

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

No data available for mRNA Expression by UniProt/SwissProt and Evidence on tissue expression from TISSUES 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
Dog
(Canis familiaris)
Mammalia HMX1 30 31
  • 91.88 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia HMX1 30 31
  • 88.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Hmx1 30
  • 83.5 (n)
Mouse
(Mus musculus)
Mammalia Hmx1 30 17 31
  • 82.53 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia HMX1 31
  • 65 (a)
OneToOne
Chicken
(Gallus gallus)
Aves HMX1 31
  • 59 (a)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia -- 31
  • 79 (a)
OneToMany
-- 31
  • 45 (a)
OneToMany
Zebrafish
(Danio rerio)
Actinopterygii LOC100333298 30
  • 69.42 (n)
hmx1 31
  • 41 (a)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Hmx 31
  • 20 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea ceh-27 31
  • 22 (a)
ManyToMany
Species where no ortholog for HMX1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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 Vase (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

ENSEMBL:
Gene Tree for HMX1 (if available)
TreeFam:
Gene Tree for HMX1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HMX1: view image

Paralogs for HMX1 Gene

Paralogs for HMX1 Gene

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

  • HMX1_HUMAN
  • F1T0J4_HUMAN
genes like me logo Genes that share paralogs with HMX1: view

Variants for HMX1 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HMX1 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
669515 Benign: not provided 8,867,861(-) T/C SYNONYMOUS_VARIANT,INTRON_VARIANT
677232 Benign: not provided 8,871,251(-) C/T MISSENSE_VARIANT
835635 Uncertain Significance: not provided 8,868,322(-) T/C MISSENSE_VARIANT,INTRON_VARIANT
845623 Uncertain Significance: not provided 8,871,494(-) T/A MISSENSE_VARIANT
846471 Uncertain Significance: not provided 8,867,916(-) C/T MISSENSE_VARIANT,INTRON_VARIANT

Additional dbSNP identifiers (rs#s) for HMX1 Gene

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

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

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)
HMX1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HMX1

SNP Genotyping and Copy Number Assay Products

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

Disorders for HMX1 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
oculoauricular syndrome
  • ocacs
anterior segment dysgenesis
  • anterior segment mesenchymal dysgenesis
entropion
microphthalmia
  • microphthalmos
cataract
  • cataracts
- elite association - COSMIC cancer census association via MalaCards
Search HMX1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

HMX1_HUMAN
  • 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.
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
  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
  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
  4. Further delineation of the oculoauricular syndrome phenotype: A new family with a novel truncating HMX1 mutation. (PMID: 29140751) Abdel-Salam GMH … Afifi HH (Ophthalmic genetics 2018) 3
  5. 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

Products for HMX1 Gene

Sources for HMX1 Gene