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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, cognitive disability, 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]
ALX4 (ALX Homeobox 4) is a Protein Coding gene. Diseases associated with ALX4 include Frontonasal Dysplasia 2 and Parietal Foramina 2. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and protein heterodimerization activity. An important paralog of this gene is ALX1.
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 |
---|---|---|---|---|---|---|---|---|---|---|
GH11J044308 | Promoter/Enhancer | 1.4 | EPDnew Ensembl ENCODE | 615.9 | +0.3 | 338 | 1.2 | ZNF512 MTA2 POLR2A REST EZH2 NRF1 ZBTB44 MGA GTF2E2 UBTF | ALX4 lnc-EXT2-2 EXT2 | |
GH11J044310 | Enhancer | 0.4 | ENCODE | 600.7 | -0.4 | -387 | 0.2 | ZNF512 EZH2 GTF2E2 | ALX4 lnc-EXT2-2 piR-48222-061 CD82 | |
GH11J044334 | Enhancer | 1.3 | Ensembl ENCODE CraniofacialAtlas | 12.2 | -24.1 | -24122 | 2.4 | LEF1 IKZF1 JUND PRDM1 DDX20 MTA2 PKNOX1 ZNF24 POLR2A MTA1 | ALX4 HSD17B12 piR-48222-061 CD82 | |
GH11J044337 | Enhancer | 0.7 | FANTOM5 CraniofacialAtlas | 14 | -27.7 | -27712 | 1.2 | IKZF1 MGA TFDP1 IRF9 RNF2 ZKSCAN8 PKNOX1 | ALX4 HSD17B12 piR-48222-061 CD82 | |
GH11J044299 | Enhancer | 0.7 | Ensembl | 12.9 | +8.6 | 8644 | 1.8 | JUND ZIC2 CEBPB SP1 SMARCC1 EGR1 ESR1 CTBP1 NR3C1 ESRRA | lnc-EXT2-2 ALX4 EXT2 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | IEA,IBA | 21873635 |
GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | ISM | 19274049 |
GO:0001228 | DNA-binding transcription activator activity, RNA polymerase II-specific | IEA,IBA | 21873635 |
GO:0003677 | DNA binding | NAS | 11137991 |
GO:0003700 | DNA-binding transcription factor activity | IEA | -- |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000790 | nuclear chromatin | ISA | -- |
GO:0005634 | nucleus | IBA,NAS | 11137991 |
GO:0005654 | nucleoplasm | IDA | -- |
GO:0005667 | transcription factor complex | IEA | -- |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0001501 | skeletal system development | NAS | 11106354 |
GO:0001942 | hair follicle development | IMP | 19692347 |
GO:0006355 | regulation of transcription, DNA-templated | IEA | -- |
GO:0006357 | regulation of transcription by RNA polymerase II | IEA | -- |
GO:0007275 | multicellular organism development | IEA | -- |
This gene was present in the common ancestor of chordates.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | ALX4 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | ALX4 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | ALX4 30 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Alx4 30 |
|
||
Mouse (Mus musculus) |
Mammalia | Alx4 30 17 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | ALX4 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | ALX4 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | ALX4 30 |
|
||
ALX-4 31 |
|
OneToOne | |||
Lizard (Anolis carolinensis) |
Reptilia | ALX4 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | alx4 30 |
|
||
African clawed frog (Xenopus laevis) |
Amphibia | Xl.16593 30 |
|
||
Zebrafish (Danio rerio) |
Actinopterygii | alx4a 30 31 |
|
OneToMany | |
alx4b 31 |
|
OneToMany |
SNP ID | Clinical significance and condition | Chr 11 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
708114 | Likely Benign: not provided | 44,267,485(-) | G/A | INTRON_VARIANT | |
710007 | Benign: Parietal foramina 2; not provided | 44,265,172(-) | C/T | SYNONYMOUS_VARIANT | |
721962 | Likely Benign: Parietal foramina 2; not provided | 44,264,908(-) | C/T | SYNONYMOUS_VARIANT | |
723592 | Likely Benign: not provided | 44,309,603(-) | A/T | MISSENSE_VARIANT | |
723770 | Likely Benign: Parietal foramina 2; not provided | 44,265,055(-) | G/A | SYNONYMOUS_VARIANT |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
dgv344e212 | CNV | loss | 25503493 |
dgv67n21 | CNV | loss | 19592680 |
esv2761670 | CNV | loss | 21179565 |
esv3547679 | CNV | deletion | 23714750 |
esv3579500 | CNV | loss | 25503493 |
esv3626160 | CNV | loss | 21293372 |
nsv832139 | CNV | loss | 17160897 |
Disorder | Aliases | PubMed IDs |
---|---|---|
frontonasal dysplasia 2 |
|
|
parietal foramina 2 |
|
|
craniosynostosis 5 |
|
|
parietal foramina |
|
|
potocki-shaffer syndrome |
|