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DLX3 distal-less homeobox 3 [ Homo sapiens (human) ]

Gene ID: 1747, updated on 11-Jun-2025
Official Symbol
DLX3provided by HGNC
Official Full Name
distal-less homeobox 3provided by HGNC
Primary source
HGNC:HGNC:2916
See related
Ensembl:ENSG00000064195 MIM:600525; AllianceGenome:HGNC:2916
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
AI4; TDO
Summary
Many vertebrate homeo box-containing genes have been identified on the basis of their sequence similarity with Drosophila developmental genes. Members of the Dlx gene family contain a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and limbs of the developing fruit fly. The Distal-less (Dlx) family of genes comprises at least 6 different members, DLX1-DLX6. Trichodentoosseous syndrome (TDO), an autosomal dominant condition, has been correlated with DLX3 gene mutation. This gene is located in a tail-to-tail configuration with another member of the gene family on the long arm of chromosome 17. Mutations in this gene have been associated with the autosomal dominant conditions trichodentoosseous syndrome and amelogenesis imperfecta with taurodontism. [provided by RefSeq, Jul 2008]
Expression
Biased expression in skin (RPKM 8.6), placenta (RPKM 4.8) and 2 other tissues See more
Orthologs
mouse all
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See DLX3 in Genome Data Viewer
Location:
17q21.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (49990005..49995224, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (50853145..50858364, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48067369..48072588, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12374 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8676 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12375 Neighboring gene RNA, U6 small nuclear 1313, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48048476-48049098 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48049099-48049721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48053397-48053960 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48053961-48054524 Neighboring gene distal-less homeobox 4 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr17:48061323-48061824 and GRCh37_chr17:48061825-48062324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48066497-48066998 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48066999-48067498 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8677 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48072293-48072875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48111925-48112721 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48125618-48126247 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48131902-48132428 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8678 Neighboring gene p53 inducible cancer associated RNA transcript 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48139516-48140016 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48140017-48140517 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr17:48141472-48142671 Neighboring gene integrin subunit alpha 3

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Homeobox gene Distal-less 3 (DLX3) is a regulator of villous cytotrophoblast differentiation. Chui A, et al. Placenta, 2011 Oct. PMID 21802725
  2. DLX3 mutation negatively regulates odontogenic differentiation of human dental pulp cells. Zeng L, et al. Arch Oral Biol, 2017 May. PMID 28135572
  3. Senescence: novel insight into DLX3 mutations leading to enhanced bone formation in Tricho-Dento-Osseous syndrome. Zhao N, et al. Sci Rep, 2016 Dec 7. PMID 27924851, Free PMC Article
  4. Increased bone density associated with DLX3 mutation in the tricho-dento-osseous syndrome. Haldeman RJ, et al. Bone, 2004 Oct. PMID 15454107
  5. Morphological analyses and a novel de novo DLX3 mutation associated with tricho-dento-osseous syndrome in a Chinese family. Li Y, et al. Eur J Oral Sci, 2015 Aug. PMID 26104267

See all (76) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association Between the Risk of Dental Caries and DLX3 Gene Polymorphisms in Chinese Children.
    Title: Association Between the Risk of Dental Caries and DLX3 Gene Polymorphisms in Chinese Children.
  2. MAST4 regulates stem cell maintenance with DLX3 for epithelial development and amelogenesis.
    Title: MAST4 regulates stem cell maintenance with DLX3 for epithelial development and amelogenesis.
  3. A novel DLX3 mutation causes tricho-dento-osseous syndrome with abnormal enamel structure and formation.
    Title: A novel DLX3 mutation causes tricho-dento-osseous syndrome with abnormal enamel structure and formation.
  4. A heterozygous missense variant in DLX3 leads to uterine leiomyomas and pregnancy losses in a consanguineous Iranian family.
    Title: A heterozygous missense variant in DLX3 leads to uterine leiomyomas and pregnancy losses in a consanguineous Iranian family.
  5. Novel DLX3 variant identified in a family with tricho-dento-osseous syndrome.
    Title: Novel DLX3 variant identified in a family with tricho-dento-osseous syndrome.
  6. Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3.
    Title: Salt Dependence of DNA Binding Activity of Human Transcription Factor Dlx3.
  7. The miR-4739/DLX3 Axis Modulates Bone Marrow-Derived Mesenchymal Stem Cell (BMSC) Osteogenesis Affecting Osteoporosis Progression.
    Title: The miR-4739/DLX3 Axis Modulates Bone Marrow-Derived Mesenchymal Stem Cell (BMSC) Osteogenesis Affecting Osteoporosis Progression.
  8. Loss of DLX3 tumor suppressive function promotes progression of SCC through EGFR-ERBB2 pathway.
    Title: Loss of DLX3 tumor suppressive function promotes progression of SCC through EGFR-ERBB2 pathway.
  9. Effects of DLX3 on the osteogenic differentiation of induced pluripotent stem cellderived mesenchymal stem cells.
    Title: Effects of DLX3 on the osteogenic differentiation of induced pluripotent stem cell‑derived mesenchymal stem cells.
  10. The data implied that DLX3 regulated Wnt/beta-catenin pathway through histone modification of DKK4 during the osteogenic differentiation of bone marrow mesenchymal stem cells.
    Title: DLX3 regulates osteogenic differentiation of bone marrow mesenchymal stem cells via Wnt/β-catenin pathway mediated histone methylation of DKK4.
Submit: New GeneRIF Correction See all GeneRIFs (56)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Hypomaturation-hypoplastic amelogenesis imperfecta with taurodontism
MedGen: C1863012 OMIM: 104510 GeneReviews: Not available
Compare labs
Tricho-dento-osseous syndrome
MedGen: C0265333 OMIM: 190320 GeneReviews: Not available
Compare labs

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in BMP signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within blood vessel development IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic skeletal system development IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in epithelial cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in hair cell differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in hair cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in hair follicle cell proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in hair follicle development IEA
Inferred from Electronic Annotation
more info
  
involved_in hair follicle morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in odontoblast differentiation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within odontogenesis of dentin-containing tooth IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within placenta development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
  
Preferred Names
homeobox protein DLX-3

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_023063.2 RefSeqGene

    Range
    5000..10219
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_005220.3 → NP_005211.1  homeobox protein DLX-3

    See identical proteins and their annotated locations for NP_005211.1

    Status: REVIEWED

    Source sequence(s)
    AC009720
    Consensus CDS
    CCDS11556.1
    UniProtKB/Swiss-Prot
    B3KQL6, O60479
    UniProtKB/TrEMBL
    B2R870
    Related
    ENSP00000389870.2, ENST00000434704.2
    Conserved Domains (3) summary
    COG5576
    Location:109 → 232
    COG5576; Homeodomain-containing transcription factor [Transcription]
    pfam00046
    Location:132 → 186
    Homeobox; Homeobox domain
    pfam12413
    Location:27 → 107
    DLL_N; Homeobox protein distal-less-like N terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    49990005..49995224 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    50853145..50858364 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O60479.1 GenPept UniProtKB/Swiss-Prot:O60479

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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