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Aliases for ALX3 Gene

Aliases for ALX3 Gene

  • ALX Homeobox 3 2 3 5
  • Proline-Rich Transcription Factor ALX3 3 4
  • Aristaless-Like Homeobox 3 2 3
  • Frontonasal Dysplasia 2 3
  • Homeobox Protein Aristaless-Like 3 3
  • FND1 3
  • FND 3

External Ids for ALX3 Gene

Previous HGNC Symbols for ALX3 Gene

  • FND

Previous GeneCards Identifiers for ALX3 Gene

  • GC01M111018
  • GC01M109469
  • GC01M109704
  • GC01M109901
  • GC01M110314
  • GC01M110404
  • GC01M110602
  • GC01M108472

Summaries for ALX3 Gene

Entrez Gene Summary for ALX3 Gene

  • This gene encodes a nuclear protein with a homeobox DNA-binding domain that functions as a transcriptional regulator involved in cell-type differentiation and development. Preferential methylation of this gene's promoter is associated with advanced-stage neuroblastoma tumors. [provided by RefSeq, Jul 2008]

GeneCards Summary for ALX3 Gene

ALX3 (ALX Homeobox 3) is a Protein Coding gene. Diseases associated with ALX3 include Frontonasal Dysplasia 1 and Cerebral Hemisphere Lipoma. Gene Ontology (GO) annotations related to this gene include sequence-specific DNA binding. An important paralog of this gene is ALX4.

UniProtKB/Swiss-Prot for ALX3 Gene

  • Transcriptional regulator with a possible role in patterning of mesoderm during development.

Additional gene information for ALX3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALX3 Gene

Genomics for ALX3 Gene

GeneHancer (GH) Regulatory Elements for ALX3 Gene

Promoters and enhancers for ALX3 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
GH01J110070 Promoter 0.7 EPDnew 650.7 +0.0 8 0.1 USF1 EZH2 ALX3 PIR35966 STRIP1
GH01J110067 Enhancer 0.4 ENCODE 0.7 +2.7 2686 0.2 SUZ12 EZH2 STRIP1 ALX3 PIR35966
GH01J110068 Enhancer 0.4 ENCODE 0.7 +2.5 2526 0.2 SUZ12 CTBP2 EZH2 ALX3 PIR35966 STRIP1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ALX3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ALX3 gene promoter:

Genomic Locations for ALX3 Gene

Genomic Locations for ALX3 Gene
10,707 bases
Minus strand

Genomic View for ALX3 Gene

Genes around ALX3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ALX3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ALX3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALX3 Gene

Proteins for ALX3 Gene

  • Protein details for ALX3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein aristaless-like 3
    Protein Accession:
    Secondary Accessions:
    • O95075
    • Q5T8M4

    Protein attributes for ALX3 Gene

    343 amino acids
    Molecular mass:
    36935 Da
    Quaternary structure:
    No Data Available

neXtProt entry for ALX3 Gene

Post-translational modifications for ALX3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ALX3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ALX3 Gene

Domains & Families for ALX3 Gene

Gene Families for ALX3 Gene

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

Protein Domains for ALX3 Gene

Suggested Antigen Peptide Sequences for ALX3 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the paired homeobox family.
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with ALX3: view

Function for ALX3 Gene

Molecular function for ALX3 Gene

UniProtKB/Swiss-Prot Function:
Transcriptional regulator with a possible role in patterning of mesoderm during development.

Phenotypes From GWAS Catalog for ALX3 Gene

Gene Ontology (GO) - Molecular Function for ALX3 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:0043565 sequence-specific DNA binding IEA --
genes like me logo Genes that share ontologies with ALX3: view
genes like me logo Genes that share phenotypes with ALX3: view

Human Phenotype Ontology for ALX3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for ALX3 Gene

MGI Knock Outs for ALX3:
  • Alx3 Alx3<tm1Hubr>

Clone Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targets and HOMER Transcription for ALX3 Gene

Localization for ALX3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALX3 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 ALX3 gene
Compartment Confidence
nucleus 5
endosome 1

Gene Ontology (GO) - Cellular Components for ALX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
genes like me logo Genes that share ontologies with ALX3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ALX3 Gene

Pathways & Interactions for ALX3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ALX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0007389 pattern specification process IEA --
genes like me logo Genes that share ontologies with ALX3: view

No data available for Pathways by source and SIGNOR curated interactions for ALX3 Gene

Drugs & Compounds for ALX3 Gene

No Compound Related Data Available

Transcripts for ALX3 Gene

mRNA/cDNA for ALX3 Gene

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

Unigene Clusters for ALX3 Gene

ALX homeobox 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALX3 Gene

No ASD Table

Relevant External Links for ALX3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ALX3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ALX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

NURSA nuclear receptor signaling pathways regulating expression of ALX3 Gene:


SOURCE GeneReport for Unigene cluster for ALX3 Gene:


Evidence on tissue expression from TISSUES for ALX3 Gene

  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for ALX3 Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • nose
  • outer ear
  • sinus
  • skull
  • tooth
  • chest wall
  • heart
  • heart valve
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with ALX3: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and mRNA Expression by UniProt/SwissProt for ALX3 Gene

Orthologs for ALX3 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALX3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ALX3 34 33
  • 99.32 (n)
(Bos Taurus)
Mammalia ALX3 34 33
  • 90.96 (n)
(Mus musculus)
Mammalia Alx3 16 34 33
  • 88.82 (n)
(Rattus norvegicus)
Mammalia Alx3 33
  • 88.44 (n)
(Canis familiaris)
Mammalia ALX3 34 33
  • 87.09 (n)
(Monodelphis domestica)
Mammalia ALX3 34
  • 79 (a)
(Ornithorhynchus anatinus)
Mammalia ALX3 34
  • 67 (a)
(Gallus gallus)
Aves ALX3 34 33
  • 74.18 (n)
(Danio rerio)
Actinopterygii LOC566955 33
  • 62.29 (n)
BX324132.5 34
  • 45 (a)
Species where no ortholog for ALX3 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)
  • lizard (Anolis carolinensis)
  • 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 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)
  • worm (Caenorhabditis elegans)

Evolution for ALX3 Gene

Gene Tree for ALX3 (if available)
Gene Tree for ALX3 (if available)
Evolutionary constrained regions (ECRs) for ALX3: view image

Paralogs for ALX3 Gene

Paralogs for ALX3 Gene

(2) SIMAP similar genes for ALX3 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with ALX3: view

Variants for ALX3 Gene

Sequence variations from dbSNP and Humsavar for ALX3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs121908166 pathogenic, Frontonasal dysplasia 1, Frontonasal dysplasia 1 (FND1) [MIM:136760] 110,061,550(-) T/C coding_sequence_variant, missense_variant
rs121908167 pathogenic, Frontonasal dysplasia 1, Frontonasal dysplasia 1 (FND1) [MIM:136760] 110,064,679(-) G/C coding_sequence_variant, missense_variant
rs121908168 pathogenic, Frontonasal dysplasia 1, Frontonasal dysplasia 1 (FND1) [MIM:136760] 110,064,634(-) G/A coding_sequence_variant, missense_variant
rs121908169 pathogenic, Frontonasal dysplasia 1 110,064,638(-) A/T coding_sequence_variant, stop_gained
rs121908170 pathogenic, Frontonasal dysplasia 1, Frontonasal dysplasia 1 (FND1) [MIM:136760] 110,064,595(-) G/A coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for ALX3 Gene

Variant ID Type Subtype PubMed ID
nsv475214 CNV novel sequence insertion 20440878

Variation tolerance for ALX3 Gene

Residual Variation Intolerance Score: 33.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.23; 24.59% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ALX3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALX3 Gene

Disorders for ALX3 Gene

MalaCards: The human disease database

(25) MalaCards diseases for ALX3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
frontonasal dysplasia 1
  • fnd1
corpus callosum lipoma
  • lipoma of the corpus callosum
cerebral hemisphere lipoma
  • lipoma of the cerebral hemisphere
basal encephalocele
maxillonasal dysplasia, binder type
  • binder syndrome
- elite association - COSMIC cancer census association via MalaCards
Search ALX3 in MalaCards View complete list of genes associated with diseases


  • Frontonasal dysplasia 1 (FND1) [MIM:136760]: The term frontonasal dysplasia describes an array of abnormalities affecting the eyes, forehead and nose and linked to midfacial dysraphia. The clinical picture is highly variable. Major findings include true ocular hypertelorism; broadening of the nasal root; median facial cleft affecting the nose and/or upper lip and palate; unilateral or bilateral clefting of the alae nasi; lack of formation of the nasal tip; anterior cranium bifidum occultum; a V-shaped or widows peak frontal hairline. {ECO:0000269 PubMed:19409524}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for ALX3

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 ALX3: view

No data available for Genatlas for ALX3 Gene

Publications for ALX3 Gene

  1. Combined restriction landmark genomic scanning and virtual genome scans identify a novel human homeobox gene, ALX3, that is hypermethylated in neuroblastoma. (PMID: 11807986) Wimmer K … Hanash SM (Genes, chromosomes & cancer 2002) 2 3 4 22 58
  2. Frontorhiny, a distinctive presentation of frontonasal dysplasia caused by recessive mutations in the ALX3 homeobox gene. (PMID: 19409524) Twigg SR … Wilkie AO (American journal of human genetics 2009) 2 3 4 58
  3. Maternal genes and facial clefts in offspring: a comprehensive search for genetic associations in two population-based cleft studies from Scandinavia. (PMID: 20634891) Jugessur A … Murray JC (PloS one 2010) 3 44 58
  4. The homeoprotein Alx3 contains discrete functional domains and exhibits cell-specific and selective monomeric binding and transactivation. (PMID: 15226305) Pérez-Villamil B … Vallejo M (The Journal of biological chemistry 2004) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for ALX3 Gene

Sources for ALX3 Gene

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