HOXD13 homeobox D13 [Homo sapiens (human)] - Gene

Summary

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: all
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Genomic context

Location:: 2q31.1

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (176087487..176095944)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (176580842..176584065)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (176957449..176960672)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.
Title: EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma.
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.
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.
Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly.
Title: Long-read whole genome sequencing reveals HOXD13 alterations in synpolydactyly.
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.
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.
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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:481600

PMC23843P1 (e-PCR)
- UniSTS:272211

PMC23843P2 (e-PCR)
- UniSTS:272212

PMC23843P3 (e-PCR)
- UniSTS:272213

Hoxd13 (e-PCR), detects polymorphism
- UniSTS:265598

HOXD13_3043 (e-PCR)
- UniSTS:462256

NoName (e-PCR)
- UniSTS:483796

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	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation more info
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	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 cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific double-stranded DNA binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in embryonic hindgut morphogenesis	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 gland development	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA-templated transcription	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 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	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment 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

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

NG_008137.1 RefSeqGene

Range

4918..8141

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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_2025_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000002.12 Reference GRCh38.p14 Primary Assembly

Range

176087487..176095944

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Conserved Domains (1) summary

pfam00046
Location:260 → 313

Homeobox; Homeobox domain
XM_011511069.3 → XP_011509371.1 homeobox protein Hox-D13 isoform X2