ALX3 Gene (Protein Coding)

ALX Homeobox 3

GC01M110059
GIFtS:
34
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] See more...

Aliases for ALX3 Gene

Aliases for ALX3 Gene

  • ALX Homeobox 3 2 3 5
  • Proline-Rich Transcription Factor ALX3 3 4
  • Homeobox Protein Aristaless-Like 3 3 4
  • Aristaless-Like Homeobox 3 2 3
  • Frontonasal Dysplasia 2 3
  • FND1 3
  • ALX3 5
  • 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 Summary 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 , Rfam classification and piRNA Summary for ALX3 Gene

Genomics for ALX3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ALX3 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
GH01J110070 Promoter 0.8 EPDnew Ensembl 600.7 0.0 -29 0.2 EZH2 USF1 ALX3 LINC01397 STRIP1 UBL4B
GH01J110068 Enhancer 0.7 Ensembl ENCODE 600.7 +1.8 1840 3.1 KDM1A POLR2A EZH2 DEK BMI1 SPI1 CBX8 ALX3 STRIP1 ENSG00000258634 piR-42967
GH01J110033 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 0.3 +35.7 35718 2.9 BRCA1 ARHGAP35 CEBPG SP1 CREB1 PRDM10 SIX5 LEF1 ZNF692 POLR2A STRIP1 LOC105378895 MN308970 ALX3
GH01J110054 Enhancer 0.9 Ensembl ENCODE 0.4 +13.3 13341 5 IKZF1 CTCF HDAC1 SOX6 NRF1 UBTF HMBOX1 EGR1 ZNF10 CEBPB ENSG00000258634 piR-46124 piR-49533 piR-47905 piR-44579 STRIP1 ALX3 MN308970
GH01J110083 Enhancer 0.8 FANTOM5 ENCODE 0.4 -13.8 -13836 1.8 RNF2 ZNF512 BACH1 PRDM1 POLR2A IRF2 EZH2 EED BCLAF1 MBD1 lnc-STRIP1-2 STRIP1 LINC01397 ALX3 UBL4B
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ALX3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ALX3

Top Transcription factor binding sites by QIAGEN in the ALX3 gene promoter:
  • CBF(2)
  • CBF-A
  • CBF-B
  • CP1A
  • E47
  • IRF-1
  • NF-Y
  • Nkx2-5
  • p300
  • Pax-4a

Genomic Locations for ALX3 Gene

Genomic Locations for ALX3 Gene
chr1:110,059,870-110,070,672
(GRCh38/hg38)
Size:
10,803 bases
Orientation:
Minus strand
chr1:110,602,616-110,613,322
(GRCh37/hg19)
Size:
10,707 bases
Orientation:
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 Structure • Gene Density

RefSeq DNA sequence for ALX3 Gene

Proteins for ALX3 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

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

    Protein Symbol:
    O95076-ALX3_HUMAN
    Recommended name:
    Homeobox protein aristaless-like 3
    Protein Accession:
    O95076
    Secondary Accessions:
    • O95075
    • Q5T8M4

    Protein attributes for ALX3 Gene

    Size:
    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

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

Protein Domains for ALX3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ALX3 Gene

GenScript: Design optimal peptide antigens:
  • Proline-rich transcription factor ALX3 (ALX3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95076

UniProtKB/Swiss-Prot:

ALX3_HUMAN :
  • Belongs to the paired homeobox family.
Family:
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with ALX3: view

Function for ALX3 Gene

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  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA 21873635
GO:0000981 DNA-binding transcription factor activity, RNA polymerase II-specific ISM 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>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ALX3

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

Nucleus.

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 ALX3 gene
Compartment Confidence
nucleus 4
extracellular 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli fibrillar center (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ALX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000790 nuclear chromatin ISA --
GO:0005634 nucleus IEA,IBA 21873635
genes like me logo Genes that share ontologies with ALX3: view

Pathways & Interactions for ALX3 Gene

PathCards logo

SuperPathways for ALX3 Gene

No Data Available

Interacting Proteins for ALX3 Gene

Selected Interacting proteins: O95076-ALX3_HUMAN for ALX3 Gene via IID

GPS-Prot Interaction Network for ALX3

Gene Ontology (GO) - Biological Process for ALX3 Gene

GO ID Qualified GO term Evidence PubMed IDs
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 --
GO:0035115 embryonic forelimb morphogenesis 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

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  1. Drug
No Compound Related Data Available

Transcripts for ALX3 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for ALX3 Gene

1 REFSEQ mRNAs :
3 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 ALX3

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

No ASD Table

Relevant External Links for ALX3 Gene

GeneLoc Exon Structure for
ALX3

Expression for ALX3 Gene

Products:

  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for ALX3 Gene
mRNA expression by GTEx for ALX3 GenemRNA expression by BioGPS for ALX3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ALX3

SOURCE GeneReport for Unigene cluster for ALX3 Gene:

Hs.669953

Evidence on tissue expression from TISSUES for ALX3 Gene

  • Nervous system(4.4)

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

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • ear
  • eye
  • eyelid
  • face
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • meninges
  • middle ear
  • mouth
  • nose
  • outer ear
  • sinus
  • skull
  • tooth
Thorax:
  • chest wall
  • heart
  • heart valve
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • 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
Chimpanzee
(Pan troglodytes)
 Mammalia ALX3 30 31
  • 99.32 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia ALX3 30 31
  • 90.96 (n)
 OneToOne
Mouse
(Mus musculus)
 Mammalia Alx3 30 17 31
  • 88.82 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Alx3 30
  • 88.44 (n)
Dog
(Canis familiaris)
 Mammalia ALX3 30 31
  • 87.09 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia ALX3 31
  • 79 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia ALX3 31
  • 67 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves ALX3 30 31
  • 74.18 (n)
 OneToOne
Zebrafish
(Danio rerio)
 Actinopterygii LOC566955 30
  • 62.29 (n)
BX324132.5 31
  • 45 (a)
 OneToOne
Species where no ortholog for ALX3 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)
  • 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 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)
  • Worm (Caenorhabditis elegans)

Evolution for ALX3 Gene

ENSEMBL:
Gene Tree for ALX3 (if available)
TreeFam:
Gene Tree for ALX3 (if available)
Aminode:
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:

  • ALX3_HUMAN
genes like me logo Genes that share paralogs with ALX3: view

Variants for ALX3 Gene

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  1. SNP Genotyping and Copy Number Assay

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ALX3 Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
4642 Pathogenic: Frontonasal dysplasia 1 110,061,565(-) T/A SPLICE_ACCEPTOR_VARIANT
711287 Benign: not provided 110,060,850(-) G/A SYNONYMOUS_VARIANT
729295 Benign: not provided 110,070,409(-) G/A SYNONYMOUS_VARIANT
738448 Likely Benign: not provided 110,060,889(-) C/T SYNONYMOUS_VARIANT
741075 Likely Benign: not provided 110,064,701(-) G/A SYNONYMOUS_VARIANT

Additional dbSNP identifiers (rs#s) for ALX3 Gene

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)
ALX3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ALX3

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

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

Disorder Aliases PubMed IDs
frontonasal dysplasia 1
  • fnd1
cerebral hemisphere lipoma
  • lipoma of the cerebral hemisphere
corpus callosum lipoma
  • lipoma of the corpus callosum
central nervous system lipoma
  • lipoma of the cns
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

UniProtKB/Swiss-Prot

ALX3_HUMAN
  • 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 widow's 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
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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
  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 41
  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
  5. Exome sequencing revealed a novel nonsense variant in ALX3 gene underlying frontorhiny. (PMID: 29215096) Ullah A … Ahmad W (Journal of human genetics 2018) 3

ExternalLinks

View latest publications for ALX3 gene in Mastermind

Products for ALX3 Gene

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