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Aliases for ALX4 Gene

Aliases for ALX4 Gene

  • ALX Homeobox 4 2 3
  • Aristaless-Like Homeobox 4 2 3
  • CRS5 3 6
  • FND2 3 6
  • Homeodomain Transcription Factor ALX4 3
  • Homeobox Protein Aristaless-Like 4 3
  • Parietal Foramina 2 2
  • KIAA1788 4
  • PFM2 6
  • FPP 6

External Ids for ALX4 Gene

Previous HGNC Symbols for ALX4 Gene

  • PFM2

Previous GeneCards Identifiers for ALX4 Gene

  • GC11P045601
  • GC11M044967
  • GC11M044321
  • GC11M044246
  • GC11M043991

Summaries for ALX4 Gene

Entrez Gene Summary for ALX4 Gene

  • This gene encodes a paired-like homeodomain transcription factor expressed in the mesenchyme of developing bones, limbs, hair, teeth, and mammary tissue. Mutations in this gene cause parietal foramina 2 (PFM2); an autosomal dominant disease characterized by deficient ossification of the parietal bones. Mutations in this gene also cause a form of frontonasal dysplasia with alopecia and hypogonadism; suggesting a role for this gene in craniofacial development, mesenchymal-epithelial communication, and hair follicle development. Deletion of a segment of chromosome 11 containing this gene, del(11)(p11p12), causes Potocki-Shaffer syndrome (PSS); a syndrome characterized by craniofacial anomalies, mental retardation, multiple exostoses, and genital abnormalities in males. In mouse, this gene has been shown to use dual translation initiation sites located 16 codons apart. [provided by RefSeq, Oct 2009]

GeneCards Summary for ALX4 Gene

ALX4 (ALX Homeobox 4) is a Protein Coding gene. Diseases associated with ALX4 include parietal foramina 2 and frontonasal dysplasia 2. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is PHOX2B.

UniProtKB/Swiss-Prot for ALX4 Gene

  • Transcription factor involved in skull and limb development. Plays an essential role in craniofacial development, skin and hair follicle development.

Gene Wiki entry for ALX4 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ALX4 Gene

Genomics for ALX4 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for ALX4 Gene

44,260,444 bp from pter
44,310,185 bp from pter
49,742 bases
Minus strand

Genomic View for ALX4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for ALX4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ALX4 Gene

Proteins for ALX4 Gene

  • Protein details for ALX4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Homeobox protein aristaless-like 4
    Protein Accession:
    Secondary Accessions:
    • Q96JN7
    • Q9H198
    • Q9HAY9

    Protein attributes for ALX4 Gene

    411 amino acids
    Molecular mass:
    44241 Da
    Quaternary structure:
    • Binds DNA.
    • Sequence=AAG23961.1; Type=Frameshift; Positions=314, 323, 340; Evidence={ECO:0000305}; Sequence=BAB47417.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for ALX4 Gene

neXtProt entry for ALX4 Gene

Proteomics data for ALX4 Gene at MOPED

Post-translational modifications for ALX4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ALX4 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for ALX4 Gene

Domains for ALX4 Gene

Gene Families for ALX4 Gene

  • PRD :Homeoboxes / PRD class

Protein Domains for ALX4 Gene

Suggested Antigen Peptide Sequences for ALX4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Q9H161
  • Contains 1 homeobox DNA-binding domain.
  • Belongs to the paired homeobox family.
genes like me logo Genes that share domains with ALX4: view

Function for ALX4 Gene

Molecular function for ALX4 Gene

UniProtKB/Swiss-Prot Function: Transcription factor involved in skull and limb development. Plays an essential role in craniofacial development, skin and hair follicle development.

Gene Ontology (GO) - Molecular Function for ALX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding NAS 11137991
GO:0003700 sequence-specific DNA binding transcription factor activity IEA --
GO:0005515 protein binding --
GO:0043565 sequence-specific DNA binding IEA --
GO:0046982 protein heterodimerization activity IEA --
genes like me logo Genes that share ontologies with ALX4: view
genes like me logo Genes that share phenotypes with ALX4: view

Animal Models for ALX4 Gene

MGI Knock Outs for ALX4:

Animal Model Products

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for ALX4

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , miRNA , Transcription Factor Targeting and HOMER Transcription for ALX4 Gene

Localization for ALX4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ALX4 Gene

Subcellular locations from

Jensen Localization Image for ALX4 Gene COMPARTMENTS Subcellular localization image for ALX4 gene
Compartment Confidence
nucleus 5

Gene Ontology (GO) - Cellular Components for ALX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus NAS 11137991
GO:0005667 transcription factor complex IEA --
genes like me logo Genes that share ontologies with ALX4: view

Pathways for ALX4 Gene

SuperPathways for ALX4 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

Gene Ontology (GO) - Biological Process for ALX4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001501 skeletal system development NAS 11106354
GO:0001942 hair follicle development IMP 19692347
GO:0006351 transcription, DNA-templated IEA --
GO:0006357 regulation of transcription from RNA polymerase II promoter --
GO:0007389 pattern specification process --
genes like me logo Genes that share ontologies with ALX4: view

No data available for Pathways by source for ALX4 Gene

Transcripts for ALX4 Gene

mRNA/cDNA for ALX4 Gene

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

Unigene Clusters for ALX4 Gene

ALX homeobox 4:
Representative Sequences:

CRISPR Products

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for ALX4

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for ALX4 Gene

No ASD Table

Relevant External Links for ALX4 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ALX4 Gene

mRNA expression in normal human tissues for ALX4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ALX4 Gene

This gene is overexpressed in Breast - Mammary Tissue (10.9), Skin - Not Sun Exposed (Suprapubic) (6.5), and Skin - Sun Exposed (Lower leg) (4.6).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for ALX4 Gene

SOURCE GeneReport for Unigene cluster for ALX4 Gene Hs.436055

mRNA Expression by UniProt/SwissProt for ALX4 Gene

Tissue specificity: Expression is likely to be restricted to bone. Found in parietal bone
genes like me logo Genes that share expressions with ALX4: view

In Situ Assay Products

Orthologs for ALX4 Gene

This gene was present in the common ancestor of chordates.

Orthologs for ALX4 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ALX4 35
  • 94.12 (n)
  • 92.23 (a)
ALX4 36
  • 98 (a)
(Bos Taurus)
Mammalia ALX4 35
  • 91.1 (n)
  • 93.7 (a)
ALX4 36
  • 93 (a)
(Canis familiaris)
Mammalia ALX4 35
  • 90.35 (n)
  • 91.73 (a)
ALX4 36
  • 93 (a)
(Mus musculus)
Mammalia Alx4 35
  • 88.39 (n)
  • 92.48 (a)
Alx4 16
Alx4 36
  • 92 (a)
(Monodelphis domestica)
Mammalia ALX4 36
  • 79 (a)
(Ornithorhynchus anatinus)
Mammalia ALX4 36
  • 58 (a)
(Rattus norvegicus)
Mammalia Alx4 35
  • 88.47 (n)
  • 91.98 (a)
(Gallus gallus)
Aves ALX-4 36
  • 77 (a)
ALX4 35
  • 79.37 (n)
  • 78.57 (a)
(Anolis carolinensis)
Reptilia ALX4 36
  • 84 (a)
African clawed frog
(Xenopus laevis)
Amphibia Xl.16593 35
tropical clawed frog
(Silurana tropicalis)
Amphibia alx4 35
  • 72.1 (n)
  • 71.93 (a)
(Danio rerio)
Actinopterygii alx4a 35
  • 70.33 (n)
  • 70.88 (a)
alx4a 36
  • 69 (a)
alx4b 36
  • 63 (a)
Species with no ortholog for ALX4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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 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)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for ALX4 Gene

Gene Tree for ALX4 (if available)
Gene Tree for ALX4 (if available)

Paralogs for ALX4 Gene

Paralogs for ALX4 Gene

Selected SIMAP similar genes for ALX4 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with ALX4: view

Variants for ALX4 Gene

Sequence variations from dbSNP and Humsavar for ALX4 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type MAF
rs168540 -- 44,266,681(-) AAGCG(C/G)CTGCT intron-variant
rs173325 -- 44,294,528(+) GAGGG(C/G)CTGGG intron-variant
rs187156 -- 44,291,917(-) ggctt(G/T)aacct intron-variant
rs193290 -- 44,267,636(-) GCTTT(A/T)TCGCG intron-variant
rs355697 -- 44,264,944(-) GAGCT(C/T)AACGG reference, synonymous-codon, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for ALX4 Gene

Variant ID Type Subtype PubMed ID
nsv832139 CNV Loss 17160897
dgv67n21 CNV Loss 19592680
nsv897303 CNV Loss 21882294
nsv897304 CNV Loss 21882294
nsv897305 CNV Loss 21882294
nsv897306 CNV Gain 21882294

Relevant External Links for ALX4 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ALX4 Gene

Disorders for ALX4 Gene

(3) OMIM Diseases for ALX4 Gene (605420)


  • Parietal foramina 2 (PFM2) [MIM:609597]: Autosomal dominant disease characterized by oval defects of the parietal bones caused by deficient ossification around the parietal notch, which is normally obliterated during the fifth fetal month. PFM2 is also a clinical feature of Potocki-Shaffer syndrome. {ECO:0000269 PubMed:11106354, ECO:0000269 PubMed:11137991}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Frontonasal dysplasia 2 (FND2) [MIM:613451]: 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:19692347}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Potocki-Shaffer syndrome (POSHS) [MIM:601224]: A syndrome characterized by foramina parietalia permagna, multiple exostoses, and craniofacial dysostosis and mental retardation in some cases. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Craniosynostosis 5 (CRS5) [MIM:615529]: A primary abnormality of skull growth involving premature fusion of one or more cranial sutures. The growth velocity of the skull often cannot match that of the developing brain resulting in an abnormal head shape and, in some cases, increased intracranial pressure, which must be treated promptly to avoid permanent neurodevelopmental disability. {ECO:0000269 PubMed:22829454}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for ALX4 Gene

(2) Novoseek inferred disease relationships for ALX4 Gene

Disease -log(P) Hits PubMed IDs
parietal foramina 97.8 1
potocki-shaffer syndrome 94.8 1

Relevant External Links for ALX4

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with ALX4: view

Publications for ALX4 Gene

  1. Haploinsufficiency of ALX4 as a potential cause of parietal foramina in the 11p11.2 contiguous gene-deletion syndrome. (PMID: 11017806) Wu Y.-Q. … Shaffer L.G. (Am. J. Hum. Genet. 2000) 2 3 4 23
  2. The ALX4 homeobox gene is mutated in patients with ossification defects of the skull (foramina parietalia permagna, OMIM 168500). (PMID: 11106354) Wuyts W. … Van Hul W. (J. Med. Genet. 2000) 3 4 23
  3. ALX4 dysfunction disrupts craniofacial and epidermal development. (PMID: 19692347) Kayserili H. … Akarsu N.A. (Hum. Mol. Genet. 2009) 3 4 23
  4. Delineation of a contiguous gene syndrome with multiple exostoses, enlarged parietal foramina, craniofacial dysostosis, and mental retardation, caused by deletions in the short arm of chromosome 11. (PMID: 8644736) Bartsch O. … Willems P.J. (Am. J. Hum. Genet. 1996) 2 3
  5. Haploinsufficiency of the human homeobox gene ALX4 causes skull ossification defects. (PMID: 11137991) Mavrogiannis L.A. … Wilkie A.O.M. (Nat. Genet. 2001) 3 4

Products for ALX4 Gene

Sources for ALX4 Gene

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