ALX3 (ALX homeobox 3)

Gene

• Entrez ID: 257
• Gene name: ALX homeobox 3
• Gene symbol: ALX3
• Synonyms (NCBI Gene): FND, FND1
• Chromosome: 1
• Chromosome location: 1p13.3
• Summary: 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

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121908166	T>C	Pathogenic	Missense variant, coding sequence variant
rs121908167	G>C	Pathogenic	Missense variant, coding sequence variant
rs121908168	G>A	Pathogenic	Missense variant, coding sequence variant
rs121908169	A>T	Pathogenic	Stop gained, coding sequence variant
rs121908170	G>A	Pathogenic	Missense variant, coding sequence variant
rs387906319	TCAG>-	Pathogenic	Coding sequence variant, frameshift variant
rs1553196068	AG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1570936479	T>A	Pathogenic	Splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT779410	hsa-miR-1587	CLIP-seq
MIRT779411	hsa-miR-1827	CLIP-seq
MIRT779412	hsa-miR-2467-3p	CLIP-seq
MIRT779413	hsa-miR-3192	CLIP-seq
MIRT779414	hsa-miR-3612	CLIP-seq
MIRT779415	hsa-miR-4257	CLIP-seq
MIRT779416	hsa-miR-4300	CLIP-seq
MIRT779417	hsa-miR-4417	CLIP-seq
MIRT779418	hsa-miR-4443	CLIP-seq
MIRT779419	hsa-miR-4492	CLIP-seq
MIRT779420	hsa-miR-4498	CLIP-seq
MIRT779421	hsa-miR-4505	CLIP-seq
MIRT779422	hsa-miR-4656	CLIP-seq
MIRT779423	hsa-miR-4675	CLIP-seq
MIRT779424	hsa-miR-4741	CLIP-seq
MIRT779425	hsa-miR-541	CLIP-seq
MIRT779426	hsa-miR-650	CLIP-seq
MIRT779427	hsa-miR-654-5p	CLIP-seq
MIRT779428	hsa-miR-762	CLIP-seq
MIRT779429	hsa-miR-920	CLIP-seq
MIRT1930032	hsa-miR-3660	CLIP-seq
MIRT1930033	hsa-miR-4526	CLIP-seq
MIRT1930034	hsa-miR-4645-3p	CLIP-seq
MIRT1930035	hsa-miR-637	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000785	Component	Chromatin	ISA
GO:0000977	Function	RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0003677	Function	DNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0007389	Process	Pattern specification process	IEA
GO:0035115	Process	Embryonic forelimb morphogenesis	IEA
GO:0035116	Process	Embryonic hindlimb morphogenesis	IEA
GO:0042981	Process	Regulation of apoptotic process	IEA
GO:0048666	Process	Neuron development	IBA
GO:0048704	Process	Embryonic skeletal system morphogenesis	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

Other IDs

• MIM: 606014
• HGNC: 449
• e!Ensembl: ENSG00000156150

Protein

• UniProt ID: O95076
• Protein name: Homeobox protein aristaless-like 3 (Proline-rich transcription factor ALX3)
• Protein function: Transcriptional regulator with a possible role in patterning of mesoderm during development.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00046	Homeodomain	154 → 210	Homeodomain	Domain

• Sequence:

  MDPEHCAPFRVGPAPGPYVASGDEPPGPQGTPAAAPHLHPAPPRGPRLTRFPACGPLEPY
  LPEPAKPPAKYLQDLGPGPALNGGHFYEGPAEAEEKTSKAASFPQLPLDCRGGPRDGPSN
  LQGSPGPCLASLHLPLSPGLPDSMELAKNKSKKRRNRTTFSTFQLEELEKVFQKTHYPDV
  YAREQLALRTDLTEARVQVWFQNRRAKWRKRERYGKIQEGRNPFTAAYDISVLPRTDSHP
  QLQNSLWASPGSGSPGGPCLVSPEGIPSPCMSPYSHPHGSVAGFMGVPAPSAAHPGIYSI
  HGFPPTLGGHSFEPSSDGDYKSPSLVSLRVKPKEPPGLLNWTT

• Sequence length: 343

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Frontorhiny	Pathogenic; Likely pathogenic	rs1570936479, rs121908166, rs121908167, rs121908169, rs387906319, rs121908170, rs2524436550, rs1553196068	RCV000004905 RCV000004906 RCV000004907 RCV000004909 RCV000004910 RCV000004911 RCV004006260 RCV000677633

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
ALX3-related disorder	Benign; Likely benign	rs150660098, rs771690383	RCV003966533 RCV003924635

Associations from Text Mining
Disease Name	Relationship Type	References
Breast Neoplasms	Inhibit	30875375
Cleft Palate	Associate	19401770
Colorectal Neoplasms	Associate	21636702
Colorectal Neoplasms	Inhibit	30875375
Frontonasal dysplasia	Associate	19409524
Rhabdomyosarcoma	Associate	22419069