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HOXD13 homeobox D13 [ Homo sapiens (human) ]

Gene ID: 3239, updated on 5-Mar-2024

Summary

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Official Symbol
HOXD13provided by HGNC
Official Full Name
homeobox D13provided by HGNC
Primary source
HGNC:HGNC:5136
See related
Ensembl:ENSG00000128714 MIM:142989; AllianceGenome:HGNC:5136
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
BDE; SPD; BDSD; SPD1; HOX4I
Summary
This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
Expression
Biased expression in colon (RPKM 2.7), prostate (RPKM 2.6) and 1 other tissue See more
Orthologs
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Genomic context

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Location:
2q31.1
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (176087487..176095944)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (176580842..176584065)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (176957449..176960672)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985830 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:176937398-176937898 Neighboring gene VISTA enhancer hs246 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:176943643-176944284 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176947449-176948064 Neighboring gene even-skipped homeobox 2 Neighboring gene NUP98-HOXD13 recombination region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:176950515-176951339 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176961670-176962253 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176962254-176962836 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176964378-176965110 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176968878-176969864 Neighboring gene homeobox D12 Neighboring gene homeobox D11 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:176980400-176981072

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Identification of a HOXD13 variant in a Mongolian family with incomplete penetrance syndactyly by exon sequencing. Husile H, et al. BMC Med Genomics, 2022 Oct 4. PMID 36195906, Free PMC Article
  2. Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly. Melas M, et al. Hum Mutat, 2022 Feb. PMID 34859533
  3. A novel microdeletion upstream of HOXD13 in a Chinese family with synpolydactyly. Jia W, et al. Am J Med Genet A, 2022 Jan. PMID 34467619
  4. Nonframeshifting indel variations in polyalanine repeat of HOXD13 gene underlies hereditary limb malformation for two Chinese families. Zu B, et al. Dev Dyn, 2021 Sep. PMID 33533119
  5. Brachydactyly type A3 is caused by a novel 13 bp HOXD13 frameshift deletion in a Chinese family. Zhang M, et al. Am J Med Genet A, 2020 Oct. PMID 32789964

See all (96) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Sequence variants in DLX5, HOXD13 and 445 kb-microduplication surrounding BTRC cause split-hand/foot malformation in three different families.
    Title: Sequence variants in DLX5, HOXD13 and 445 kb-microduplication surrounding BTRC cause split-hand/foot malformation in three different families.
  2. HOXD13-associated synpolydactyly: Extending and validating the genotypic and phenotypic spectrum with 38 new and 49 published families.
    Title: HOXD13-associated synpolydactyly: Extending and validating the genotypic and phenotypic spectrum with 38 new and 49 published families.
  3. Variants Identified in the HOXC13 and HOXD13 Genes Suggest Association with Cervical Cancer in a Cohort of Mexican Women.
    Title: Variants Identified in the HOXC13 and HOXD13 Genes Suggest Association with Cervical Cancer in a Cohort of Mexican Women.
  4. EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.
    Title: EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.
  5. Identification of a HOXD13 variant in a Mongolian family with incomplete penetrance syndactyly by exon sequencing.
    Title: Identification of a HOXD13 variant in a Mongolian family with incomplete penetrance syndactyly by exon sequencing.
  6. Novel HOXD13 variants in syndactyly type 1b and type 1c, and a new spectrum of TP63-related disorders.
    Title: Novel HOXD13 variants in syndactyly type 1b and type 1c, and a new spectrum of TP63-related disorders.
  7. Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly.
    Title: Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly.
  8. A novel microdeletion upstream of HOXD13 in a Chinese family with synpolydactyly.
    Title: A novel microdeletion upstream of HOXD13 in a Chinese family with synpolydactyly.
  9. Nonframeshifting indel variations in polyalanine repeat of HOXD13 gene underlies hereditary limb malformation for two Chinese families.
    Title: Nonframeshifting indel variations in polyalanine repeat of HOXD13 gene underlies hereditary limb malformation for two Chinese families.
  10. HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
    Title: HOXD13 promotes the malignant progression of colon cancer by upregulating PTPRN2.
Submit: New GeneRIF Correction See all GeneRIFs (60)

Phenotypes

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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
Brachydactyly type D
MedGen: C0220664 OMIM: 113200 GeneReviews: Not available
Compare labs
Brachydactyly type E1
MedGen: C1862102 OMIM: 113300 GeneReviews: Not available
Compare labs
Brachydactyly-syndactyly syndrome
MedGen: C1853137 OMIM: 610713 GeneReviews: Not available
Compare labs
Syndactyly type 5
MedGen: C1861348 OMIM: 186300 GeneReviews: Not available
Compare labs
Synpolydactyly type 1
MedGen: C5574994 OMIM: 186000 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-09-23)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2020-09-23)

ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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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 transcription activator activity, RNA polymerase II-specific IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
  
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 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 chromatin binding IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in anterior/posterior pattern specification IEA
Inferred from Electronic Annotation
more info
  
involved_in branch elongation of an epithelium IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic digit morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in embryonic hindgut morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in male genitalia development IEA
Inferred from Electronic Annotation
more info
  
involved_in morphogenesis of an epithelial fold IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of DNA-templated transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in regulation of branching involved in prostate gland morphogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of cell population proliferation 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
  
involved_in response to testosterone IEA
Inferred from Electronic Annotation
more info
  
involved_in skeletal system development IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  

General protein information

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Preferred Names
homeobox protein Hox-D13
Names
homeo box 4I
homeo box D13
homeobox protein Hox-4I
synpolydactyly

NCBI Reference Sequences (RefSeq)

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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_008137.1 RefSeqGene

    Range
    4918..8141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000523.4 → NP_000514.2  homeobox protein Hox-D13

    See identical proteins and their annotated locations for NP_000514.2

    Status: REVIEWED

    Source sequence(s)
    AC009336, BX100910
    Consensus CDS
    CCDS2264.2
    UniProtKB/Swiss-Prot
    P35453
    Related
    ENSP00000376322.3, ENST00000392539.4
    Conserved Domains (2) summary
    cd00086
    Location:277 → 333
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
    pfam12284
    Location:39 → 174
    HoxA13_N; Hox protein A13 N terminal

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    176087487..176095944
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511068.3 → XP_011509370.1  homeobox protein Hox-D13 isoform X1

    Conserved Domains (1) summary
    pfam00046
    Location:260 → 313
    Homeobox; Homeobox domain

  2. XM_011511069.3 → XP_011509371.1  homeobox protein Hox-D13 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    176580842..176584065
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P35453.3 GenPept UniProtKB/Swiss-Prot:P35453

Gene LinkOut

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