HOXD13

gene
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Summary

HOXD13 (homeobox D13, HGNC:5136) is a protein-coding gene on chromosome 2q31.1, encoding Homeobox protein Hox-D13 (P35453). Sequence-specific transcription factor that binds gene promoters and activates their transcription. It is a selective cancer dependency (DepMap: 13.8% of cell lines) and haploinsufficient (ClinGen: sufficient evidence).

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.

Source: NCBI Gene 3239 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): brachydactyly-syndactyly syndrome (Definitive, GenCC) — +5 more curated relationships
  • GWAS associations: 1
  • Clinical variants (ClinVar): 188 total — 28 pathogenic, 3 likely-pathogenic
  • Phenotypes (HPO): 97
  • Cancer dependency (DepMap): dependent in 13.8% of screened cell lines
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • Transcription factor: yes — 21 downstream targets (CollecTRI)
  • MANE Select transcript: NM_000523

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:5136
Approved symbolHOXD13
Namehomeobox D13
Location2q31.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000128714
Ensembl biotypeprotein_coding
OMIM142989
Entrez3239

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000392539

RefSeq mRNA: 1 — MANE Select: NM_000523 NM_000523

CCDS: CCDS2264

Canonical transcript exons

ENST00000392539 — 2 exons

ExonStartEnd
ENSE00000882905176092721176093671
ENSE00001272192176094480176095944

Expression profiles

Bgee: expression breadth broad, 47 present calls, max score 82.98.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4270 / max 42.4460, expressed in 135 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
238170.184459
238180.150383
238160.092354

Top tissues by expression

274 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
urethraUBERON:000005782.98gold quality
vaginaUBERON:000099682.65gold quality
muscle layer of sigmoid colonUBERON:003580581.57gold quality
ectocervixUBERON:001224981.50gold quality
calcaneal tendonUBERON:000370179.12gold quality
sigmoid colonUBERON:000115977.63gold quality
seminal vesicleUBERON:000099876.66gold quality
prostate glandUBERON:000236775.79gold quality
endocervixUBERON:000045874.27gold quality
mammalian vulvaUBERON:000099771.50gold quality
tendonUBERON:000004369.57gold quality
rectumUBERON:000105269.33gold quality
uterine cervixUBERON:000000267.64gold quality
parotid glandUBERON:000183167.10gold quality
endothelial cellCL:000011565.85gold quality
heart right ventricleUBERON:000208065.00gold quality
nasal cavity epitheliumUBERON:000538464.80gold quality
buccal mucosa cellCL:000233664.52gold quality
colonic mucosaUBERON:000031760.60silver quality
mucosa of sigmoid colonUBERON:000499360.47silver quality
lower lobe of lungUBERON:000894960.37silver quality
skeletal muscle tissue of biceps brachiiUBERON:000450260.26gold quality
secondary oocyteCL:000065559.43gold quality
vastus lateralisUBERON:000137958.99gold quality
quadriceps femorisUBERON:000137758.98gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451158.60gold quality
pericardiumUBERON:000240758.24gold quality
large intestineUBERON:000005958.03gold quality
colonUBERON:000115557.83gold quality
cerebellar vermisUBERON:000472057.64gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-MTAB-8060yes721.04
E-ANND-3no1.14

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

21 targets.

TargetRegulation
BARX1Repression
BMP2
BMP4Activation
CASP8AP2
CYP1A1
DACH1Activation
EMX2
EPHA3Repression
EPHA4Repression
EPHA7Activation
FBN1Activation
FHL1Unknown
H1-6
HAND2Activation
HOXA13
HOXD13
IL6
NGEF
SALL1Repression
SALL3Repression
SFRP1

JASPAR motifs

MotifNameFamily
MA0909.1HOXD13HOX
MA0909.2HOXD13HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): EZH2, FOXC1, GLI3, HOXD13, MYC

miRNA regulators (miRDB)

128 targeting HOXD13, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-548N99.9871.944170
HSA-MIR-56899.9869.862084
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4715-3P99.9866.03670
HSA-MIR-60799.9773.625593
HSA-MIR-4725-3P99.9669.532520
HSA-MIR-6780B-5P99.9669.602562
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-568899.9673.234504
HSA-MIR-495-3P99.9672.814197
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-570-3P99.9672.414910
HSA-MIR-55999.9572.283609
HSA-MIR-548AB99.9571.313488
HSA-MIR-548A-5P99.9471.273482
HSA-MIR-548AD-5P99.9471.233502
HSA-MIR-548AE-5P99.9471.233502
HSA-MIR-548AK99.9471.243488
HSA-MIR-548AM-5P99.9471.243488
HSA-MIR-548AP-5P99.9471.143489
HSA-MIR-548AQ-5P99.9471.343426
HSA-MIR-548AR-5P99.9471.283515
HSA-MIR-548AS-5P99.9471.223482
HSA-MIR-548AU-5P99.9471.243488
HSA-MIR-548AY-5P99.9471.233502

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 13.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 40)

  • 117-kb microdeletion removing HOXD9-HOXD13 and EVX2 causes synpolydactyly (PMID:11778160)
  • Data show that a mutant HOXD13 protein that recognizes only a subset of sites recognized by the wild-type protein causes a novel human limb malformation. (PMID:12620993)
  • Missense mutations in this protein are associated with brachydactyly types D and E. (PMID:12649808)
  • This is the first report on prenatal diagnosis of Synpolydactyly by detecting the HOXD13 polyalanine expansion in the Han population of the Chinese mainland. (PMID:15696469)
  • Results suggest that synpolydactyly in this kindred may be caused by polyalanine expansion in HOXD13. (PMID:15952114)
  • Data show that HOXD13 are important susceptible genes of idiopathic congenital talipes equinovarus. (PMID:16331564)
  • synergism between NUP98-HOX and wt-Flt3 is the result of the ability of Flt3 to increase proliferation of myeloid progenitors blocked in differentiation by NUP98-HOX fusions, revealing a direct role for wt-Flt3 in the pathobiology of AML. (PMID:16861351)
  • There is a link between HOXD13 and two additional limb phenotypes–syndactyly type V and brachydactyly type A4–and demonstrated that a polyalanine contraction in HOXD13, most likely, led to other digital anomalies but not to synpolydactyly. (PMID:17236141)
  • findings strongly suggest that specific mutations in HOXD13 gene may cause both hypoplastic synpolydactyly and hypospadias (PMID:17656229)
  • Early human development shows spatiotemporal differences of HOXD13 expression in the endodermal and mesodermal structures. (PMID:17853405)
  • We showed that SPD1 phenotype segregates with an identical expansion mutation of 21 bp in HOXD13. We show that HOXD13 polyalanine repeat is polymorphic, and the expansion of 2 alanine residues, is without clinical consequences. (PMID:18072967)
  • The results shows that HOXD13 gene mutation was not involved in outbreak in idiopathic congenital talipes equinovarus, but changes of HOXD13 and FHL1 gene expression related to the development of talipes equinovarus malformation. (PMID:18244901)
  • analysis of HOXD13 in 100 patients with limb malformations; 7 novel mutations in the coding region & 2 novel mutations in the 5’-untranslated region were identified (PMID:18399101)
  • transgenic mice expressing NUP98-HOXD13 (NHD13) fusion gene develop myelodysplastic syndrome, and more than half eventually progress to acute leukemia (PMID:18566322)
  • Hoxd13 and Fhl1 were expressed in the interdigital tissues of E12.5 rat embryo. Luciferase assay and EMSA identified a novel promoter region of Fhl1 that directly interacts with Hoxd13 (PMID:18758158)
  • G220V missense mutation of HOXD13 caused synpolydactyly in a Greek family. (PMID:19060004)
  • Detection of the HOXD13 homeoprotein in pancreas-tissue microarrays shows that its negative expression has a significant and adverse effect on the prognosis of patients with pancreatic cancer. (PMID:19488988)
  • data show no significant difference in HOXD11, HOXD12 & HOXD13 genotype frequencies between the autism spectrum disorder & healthy controls, but one SNP in promoter region of HOXD11 was observed in only 4 patients with ASD (PMID:19540081)
  • results expand the spectrum of HOXD13 mutations;suggest that not only the size of the polyalanine repeat but also other unknown factors might play a role in synpolydactyly (PMID:19686284)
  • Geminin, which interacts with HOXD13 as well, blocks HOXD13-mediated assembly of pre-replication complex proteins and inhibits HOXD13-induced DNA replication. (PMID:19703996)
  • a duplication mutation, c. 186-212dup, in exon 1 of the HOXD13 gene in the affected individuals in a Chinese family with unusual clinical manifestations of synpolydactyly (PMID:20974300)
  • Variable skeletal phenotype in 2q31 deletion patients is a result of hemizygosity for the HOXD genes. (PMID:21068127)
  • results show the first nonsense mutation in the HOXD13 gene underlying a severe form of SPD in the homozygous state, and a milder form of SPD with approximately 50% penetrance in the heterozygous state. (PMID:21814222)
  • HOXD13 gene mutation was responsible for the synpolydactyly (SPD) phenotype in this family. (PMID:22161087)
  • Misexpression of HOXD13(G11A) in the developing chick limb phenocopied the human SPD phenotype (PMID:22373878)
  • This finding expands the phenotypic spectrum associated with HOXD13 mutations and advances our understanding of human limb development. (PMID:22374128)
  • Correlation between Synpolydactyly and alanine expansion in HOXD13. (PMID:22406499)
  • findings show that expression of NUP98-HOXD13 impairs class switch recombination and reduces the antibody-mediated immune response, in addition to its role in leukemia (PMID:22613470)
  • Identification of a novel c.659G>C (p.Gly220Ala) mutation outside the HOXD13 homeodomain responsible for synpolydactyly in a Chinese family. (PMID:23948678)
  • Data indicate increased levels of reactive oxygen species (ROS) were detected in bone marrow nucleated cells (BMNC) that express CD71 in in NUP98-HOXD13 (NHD13) transgenic mice, a murine model for myelodysplastic syndromes (MDS). (PMID:23958061)
  • A genome-wide array-comparative genomic hybridization (aCGH) analysis revealed global chromosomal aberration in MWCNTs-treated clones, predominantly at chromosome 2q31-32, where the potential oncogenes HOXD9 and HOXD13 are located (PMID:23984819)
  • Molecular characteristics of a HOXD13 synpolydactyly 1 nonsense mutation in a Chinese family. (PMID:24055421)
  • Linkage analysis of the syndactyly type 1 subtype c (SD1-c) phenotype based on two Chinese families with 3/4 fingers syndactyly shows that two missense mutations in codon 306 of HOXD13 underlie SD1-c. (PMID:24789103)
  • A 27 bp expansion mutation in exon 1 of HOXD13 was associated with autosomal dominant synpolydactyly in a Chinese family. (PMID:26252089)
  • A homozygous HOXD13 missense mutation causes a severe form of synpolydactyly with metacarpal to carpal transformation. (PMID:26581570)
  • HOXD13 methylation is a common event in primary breast cancer and is associated with poor survival of breast cancer patients. (PMID:26617782)
  • down-regulation of HOXD13 might be a potentially useful prognostic marker for patients with breast cancer. (PMID:26617867)
  • a novel mutation causing truncation of HOXD13 protein was successfully identified as being associated with an atypical non-syndromic SPD phenotype in our study. (PMID:27254532)
  • Knock down of the dickkopf WNT signaling pathway inhibitor 2 (DKK2) resulted in a significant suppression of HOXD10, HOXD11 and HOXD13 while over-expression of DKK2 and stimulation with factors of the WNT signaling pathway. (PMID:27363011)
  • The results suggest that the c.917G>A (p.R306Q) mutation in the HOXD13 gene, may be responsible for syndactyly type Ic in this family. (PMID:28498426)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusHoxd13ENSMUSG00000001819
rattus_norvegicusHoxd13ENSRNOG00000001588

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD3 (ENSG00000128652), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-D13P35453 (reviewed: P35453)

Alternative names: Homeobox protein Hox-4I

All UniProt accessions (1): P35453

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor that binds gene promoters and activates their transcription. Part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Subcellular location. Nucleus.

Disease relevance. Synpolydactyly 1 (SPD1) [MIM:186000] Limb malformation that shows a characteristic manifestation in both hands and feet. This condition is inherited as an autosomal dominant trait with reduced penetrance. The disease is caused by variants affecting the gene represented in this entry. Brachydactyly D (BDD) [MIM:113200] A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type D is characterized by short and broad terminal phalanges of the thumbs and big toes. The disease is caused by variants affecting the gene represented in this entry. Syndactyly 5 (SDTY5) [MIM:186300] A form of syndactyly, a congenital anomaly of the hand or foot marked by persistence of the webbing between adjacent digits that are more or less completely attached. The characteristic finding in SDTY5 is the presence of an associated metacarpal and metatarsal fusion. The metacarpals and metatarsals most commonly fused are the 4th and 5th or the 3rd and 4th. Soft tissue syndactyly usually affects the 3rd and 4th fingers and the 2nd and 3rd toes. The disease is caused by variants affecting the gene represented in this entry. Brachydactyly-syndactyly syndrome (BDSD) [MIM:610713] A disease characterized by generalized shortening of the hands and feet, broad and short distal phalanges of the thumbs, and cutaneous syndactyly of toes 2 and 3. The limb phenotypes observed in this syndrome overlap those of brachydactyly types A4, D, E and syndactyly type 1. The disease is caused by variants affecting the gene represented in this entry. Brachydactyly E1 (BDE1) [MIM:113300] A form of brachydactyly. Brachydactyly defines a group of inherited malformations characterized by shortening of the digits due to abnormal development of the phalanges and/or the metacarpals. Brachydactyly type E is characterized by shortening of the fingers mainly in the metacarpals and metatarsals. Wide variability in the number of digits affected occurs from person to person, even in the same family. Some individuals are moderately short of stature. Brachydactyly type E1 is characterized by shortening limited to fourth metacarpals and/or metatarsals. The disease is caused by variants affecting the gene represented in this entry. VACTERL association (VACTERL) [MIM:192350] VACTERL is an acronym for vertebral anomalies, anal atresia, congenital cardiac disease, tracheoesophageal fistula, renal anomalies, radial dysplasia, and other limb defects. The gene represented in this entry may be involved in disease pathogenesis. Brachydactyly-syndactyly-oligodactyly syndrome (BDSDO) [MIM:610713] A syndrome characterized by a complex brachydactyly-syndactyly-oligodactyly phenotype. Limb anomalies include reduced number of digits that are severely shortened, camptodactyly, syndactyly, absence of terminal phalanges of the thumbs, and absence of nails of the thumbs and toes. The disease is caused by variants affecting the gene represented in this entry.

Polymorphism. The poly-Ala region is polymorphic (11 to 15 residues) in the normal population and is expanded to about 22-29 residues in SPD1 and syndactyly type 5 patients.

Similarity. Belongs to the Abd-B homeobox family.

RefSeq proteins (1): NP_000514* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001356HDDomain
IPR009057Homeodomain-like_sfHomologous_superfamily
IPR017970Homeobox_CSConserved_site
IPR022067HoxA13_NDomain
IPR051003AP_axis_regulatory_HomeoboxFamily

Pfam: PF00046, PF12284

UniProt features (17 total): sequence variant 12, region of interest 2, chain 1, DNA-binding region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P35453-F157.180.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 453 (showing top): GSE18804_BRAIN_VS_COLON_TUMORAL_MACROPHAGE_DN, GSE45365_NK_CELL_VS_CD8A_DC_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, GOBP_MORPHOGENESIS_OF_AN_EPITHELIUM, GOBP_EPITHELIUM_DEVELOPMENT, BENPORATH_ES_WITH_H3K27ME3, GOBP_GLAND_MORPHOGENESIS, GOBP_REGULATION_OF_MORPHOGENESIS_OF_A_BRANCHING_STRUCTURE, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_PROSTATE_GLAND_MORPHOGENESIS, GOBP_EMBRYONIC_DIGIT_MORPHOGENESIS, GOBP_MALE_GENITALIA_DEVELOPMENT, GOBP_BRANCH_ELONGATION_OF_AN_EPITHELIUM, GOBP_GROWTH, GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN

GO Biological Process (20): skeletal system development (GO:0001501), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), transcription by RNA polymerase II (GO:0006366), anterior/posterior pattern specification (GO:0009952), male genitalia development (GO:0030539), response to testosterone (GO:0033574), regulation of cell population proliferation (GO:0042127), embryonic digit morphogenesis (GO:0042733), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic hindgut morphogenesis (GO:0048619), prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527), morphogenesis of an epithelial fold (GO:0060571), branch elongation of an epithelium (GO:0060602), regulation of branching involved in prostate gland morphogenesis (GO:0060687), pattern specification process (GO:0007389), gland morphogenesis (GO:0022612), embryonic limb morphogenesis (GO:0030326), prostate gland development (GO:0030850), limb morphogenesis (GO:0035108)

GO Molecular Function (8): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), DNA binding (GO:0003677), chromatin binding (GO:0003682), DNA-binding transcription factor activity (GO:0003700), sequence-specific double-stranded DNA binding (GO:1990837), cis-regulatory region sequence-specific DNA binding (GO:0000987)

GO Cellular Component (3): chromatin (GO:0000785), nucleoplasm (GO:0005654), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
RNA polymerase II transcription regulatory region sequence-specific DNA binding3
DNA-templated transcription2
regulation of DNA-templated transcription2
transcription by RNA polymerase II2
embryonic morphogenesis2
regulation of transcription by RNA polymerase II2
branching involved in prostate gland morphogenesis2
gland development2
transcription cis-regulatory region binding2
cellular anatomical structure2
system development1
regulation of gene expression1
regulation of RNA biosynthetic process1
regionalization1
male sex differentiation1
genitalia development1
reproductive system development1
response to lipid1
response to ketone1
cell population proliferation1
regulation of cellular process1
embryonic limb morphogenesis1
positive regulation of DNA-templated transcription1
hindgut morphogenesis1
prostate glandular acinus morphogenesis1
morphogenesis of an epithelium1
axis elongation1
morphogenesis of a branching epithelium1
regulation of morphogenesis of a branching structure1
regulation of morphogenesis of an epithelium1
regulation of reproductive process1
multicellular organism development1
multicellular organismal process1
animal organ morphogenesis1
limb morphogenesis1
embryonic appendage morphogenesis1
urogenital system development1
reproductive structure development1
appendage morphogenesis1
limb development1

Protein interactions and networks

STRING

1294 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
HOXD13SHHQ15465869
HOXD13SPDL1Q96EA4868
HOXD13NUP98P52948829
HOXD13CD274Q9NZQ7726
HOXD13PDCD1LG2Q9BQ51702
HOXD13PRRX1P54821674
HOXD13FBLN1P23142663
HOXD13PHF23Q9BUL5641
HOXD13SHOX2O60902633
HOXD13GLI3P10071627
HOXD13DDX10Q13206621
HOXD13PRSS53Q2L4Q9605
HOXD13HOXD10P28358600
HOXD13ZP2Q05996599
HOXD13HOXD11P31277593

IntAct

53 interactions, top by confidence:

ABTypeScore
TNFSF14TMEM11psi-mi:“MI:0914”(association)0.670
JUNNFATC1psi-mi:“MI:0914”(association)0.610
IL13RA2METTL15psi-mi:“MI:0914”(association)0.530
SLC2A12METTL15psi-mi:“MI:0914”(association)0.530
PLAURXRCC3psi-mi:“MI:0914”(association)0.530
GPR55LGALS3psi-mi:“MI:0914”(association)0.530
DGCR2HOXD13psi-mi:“MI:0914”(association)0.530
HOXD13EEF1Dpsi-mi:“MI:0914”(association)0.530
CREB1NFIXpsi-mi:“MI:0914”(association)0.350
FOSNFIXpsi-mi:“MI:0914”(association)0.350
FOXA1NFICpsi-mi:“MI:0914”(association)0.350
FOXA2FOXN2psi-mi:“MI:0914”(association)0.350
FOXA3DDX39Apsi-mi:“MI:0914”(association)0.350
FOXB1DDX39Apsi-mi:“MI:0914”(association)0.350
FOXC1NFIXpsi-mi:“MI:0914”(association)0.350
FOXC2ZNF536psi-mi:“MI:0914”(association)0.350
FOXE1DDX39Apsi-mi:“MI:0914”(association)0.350
FOXF1HOXB9psi-mi:“MI:0914”(association)0.350
FOXI2DDX39Apsi-mi:“MI:0914”(association)0.350
FOXJ2TCERG1psi-mi:“MI:0914”(association)0.350
FOXN1FOXN1psi-mi:“MI:0914”(association)0.350
FOXQ1DDX39Apsi-mi:“MI:0914”(association)0.350
RBPJSAMD1psi-mi:“MI:0914”(association)0.350
JUNpsi-mi:“MI:0914”(association)0.350
PB1ESYT2psi-mi:“MI:0914”(association)0.350
F9DDX11L8psi-mi:“MI:0914”(association)0.350
RPS16MCRIP1psi-mi:“MI:0914”(association)0.350
IQCNTARS3psi-mi:“MI:0914”(association)0.350

BioGRID (85): HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS), HOXD13 (Affinity Capture-MS)

ESM2 similar proteins: A1A5R1, A2YXQ1, A4F5G6, A6NFN3, A6QPR6, E3WDQ9, O42366, O43251, O65034, O80416, P24344, P35453, P46609, P55316, P56260, P70217, Q00939, Q02962, Q0VD23, Q14671, Q17QD3, Q1A1A1, Q1A1A2, Q1A1A3, Q1A1A4, Q1A1A5, Q1A1A6, Q1KKX5, Q27002, Q2VB19, Q5NVN8, Q5R5X3, Q60987, Q642J5, Q66JB7, Q66KI6, Q6YHU8, Q6ZBH6, Q6ZK57, Q7TN99

Diamond homologs: A1YFT7, A2D5V0, A2D635, A2T6F8, A2T7D1, A2T7H7, G5EFY5, O14627, O42502, O42506, O43248, P02835, P09013, P09067, P09079, P09087, P09631, P09633, P10038, P10179, P17482, P17919, P20615, P23812, P24061, P24341, P24342, P24343, P24344, P28358, P28359, P31257, P31260, P31263, P31268, P31269, P31271, P31272, P31274, P31275

SIGNOR signaling

2 interactions.

AEffectBMechanism
HOXD13“up-regulates quantity by expression”EPHA7“transcriptional regulation”
HOXD13“up-regulates activity”MEIS1binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 74 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
somitogenesis633.0×4e-06
anatomical structure morphogenesis918.4×4e-07
Notch signaling pathway612.5×7e-04
chromatin organization68.8×4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

188 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic28
Likely pathogenic3
Uncertain significance106
Likely benign18
Benign17

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1332838NM_000523.4(HOXD13):c.708del (p.Asn236fs)Pathogenic
1451293NM_000523.4(HOXD13):c.186_212dup (p.Ala63_Ala71dup)Pathogenic
1452333NM_000523.4(HOXD13):c.542_552del (p.Asn181fs)Pathogenic
1453451NM_000523.4(HOXD13):c.314_315del (p.Lys105fs)Pathogenic
14867NM_000523.4(HOXD13):c.323_336del (p.Pro108fs)Pathogenic
14868NM_000523.4(HOXD13):c.834del (p.Lys279fs)Pathogenic
14869NM_000523.4(HOXD13):c.964A>C (p.Ile322Leu)Pathogenic
14871NM_000523.4(HOXD13):c.782-2delPathogenic
14873NM_000523.4(HOXD13):c.209_210insGGCTGCGGCGGCGGCAGCGGC (p.Ala65_Ala71dup)Pathogenic
14874NM_000523.4(HOXD13):c.974A>G (p.Gln325Arg)Pathogenic
14875NM_000523.4(HOXD13):c.183_203del (p.Ala65_Ala71del)Pathogenic
14876NM_000523.4(HOXD13):c.683G>T (p.Gly228Val)Pathogenic
1919465NM_000523.4(HOXD13):c.183_203dup (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAla)Pathogenic
225650NM_000523.4(HOXD13):c.742C>T (p.Gln248Ter)Pathogenic
225652NM_000523.4(HOXD13):c.917G>A (p.Arg306Gln)Pathogenic
225653NM_000523.4(HOXD13):c.781+1G>APathogenic
225654NM_000523.4(HOXD13):c.683G>C (p.Gly228Ala)Pathogenic
225655NM_000523.4(HOXD13):c.973C>A (p.Gln325Lys)Pathogenic
225656NM_000523.4(HOXD13):c.916C>G (p.Arg306Gly)Pathogenic
2502140NM_000523.4(HOXD13):c.684dup (p.Tyr229fs)Pathogenic
3252671NM_000523.4(HOXD13):c.206_207insAGCGGCGGCTGCGGCGGCGGCAGC (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAlaAla)Pathogenic
3256389NM_000523.4(HOXD13):c.212_213insTGCCGCCGCCGCAGCCGCCGCTGCCGC (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAlaAlaAla)Pathogenic
3346356NM_000523.4(HOXD13):c.858del (p.Gln287fs)Pathogenic
3382450NM_000523.4(HOXD13):c.673del (p.Ser225fs)Pathogenic
3728565NM_000523.4(HOXD13):c.663_664del (p.Glu221fs)Pathogenic
4271933NM_000523.4(HOXD13):c.461C>A (p.Ser154Ter)Pathogenic
689765NM_000523.4(HOXD13):c.744_747del (p.Gln248fs)Pathogenic
916250NM_000523.4(HOXD13):c.212_213insGGCGGCTGCGGCGGCGGCAGCGGCAGC (p.Ala63_Ala71dup)Pathogenic
1324539NM_000523.4(HOXD13):c.203_204insA (p.Ala69fs)Likely pathogenic
2499278NM_000523.4(HOXD13):c.938C>G (p.Thr313Arg)Likely pathogenic

SpliceAI

179 predictions. Top by Δscore:

VariantEffectΔscore
2:176094477:CAG:Cacceptor_loss1.0000
2:176094478:AGG:Aacceptor_gain1.0000
2:176094479:GGG:Gacceptor_gain1.0000
2:176093667:TCCAG:Tdonor_loss0.9900
2:176093668:CCAG:Cdonor_loss0.9900
2:176093669:CAGGT:Cdonor_loss0.9900
2:176093670:AGGTA:Adonor_loss0.9900
2:176093671:GG:Gdonor_loss0.9900
2:176093672:GT:Gdonor_loss0.9900
2:176093673:T:Adonor_loss0.9900
2:176094468:T:TAacceptor_gain0.9900
2:176094475:A:AGacceptor_gain0.9900
2:176094475:ATCAG:Aacceptor_gain0.9900
2:176094476:T:Gacceptor_gain0.9900
2:176094478:A:AGacceptor_gain0.9900
2:176094478:AG:Aacceptor_gain0.9900
2:176094478:AGGG:Aacceptor_gain0.9900
2:176094479:G:GGacceptor_gain0.9900
2:176094479:GG:Gacceptor_gain0.9900
2:176094479:GGGG:Gacceptor_gain0.9900
2:176093455:G:GTdonor_gain0.9800
2:176094472:T:Aacceptor_gain0.9800
2:176093576:ACC:Adonor_gain0.9700
2:176094472:T:TAacceptor_loss0.9700
2:176094476:TCAGG:Tacceptor_gain0.9700
2:176094477:CA:Cacceptor_gain0.9700
2:176094478:A:Cacceptor_gain0.9700
2:176094479:GGGGA:Gacceptor_gain0.9700
2:176094474:TATCA:Tacceptor_gain0.9600
2:176094479:G:Tacceptor_gain0.9600

AlphaMissense

2191 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:176094528:G:TR277M1.000
2:176094529:G:CR277S1.000
2:176094529:G:TR277S1.000
2:176094530:A:GK278E1.000
2:176094532:G:CK278N1.000
2:176094532:G:TK278N1.000
2:176094537:G:CR280T1.000
2:176094538:A:CR280S1.000
2:176094538:A:TR280S1.000
2:176094543:C:AP282H1.000
2:176094545:T:AY283N1.000
2:176094545:T:CY283H1.000
2:176094545:T:GY283D1.000
2:176094546:A:GY283C1.000
2:176094549:C:TT284I1.000
2:176094558:A:GQ287R1.000
2:176094559:G:CQ287H1.000
2:176094559:G:TQ287H1.000
2:176094561:T:AL288H1.000
2:176094561:T:CL288P1.000
2:176094570:T:AL291Q1.000
2:176094570:T:CL291P1.000
2:176094570:T:GL291R1.000
2:176094573:A:TE292V1.000
2:176094574:G:CE292D1.000
2:176094574:G:TE292D1.000
2:176094581:T:CY295H1.000
2:176094581:T:GY295D1.000
2:176094582:A:CY295S1.000
2:176094582:A:GY295C1.000

dbSNP variants (sampled 300 via entrez): RS1000616285 (2:176091021 C>T), RS1000890848 (2:176091280 G>A), RS1000944462 (2:176095478 T>G), RS1000977286 (2:176095710 T>A), RS1000986290 (2:176086701 G>A), RS1001133189 (2:176089709 G>A,C), RS1001164454 (2:176091985 T>C), RS1001216914 (2:176092288 G>A), RS1001303211 (2:176089178 C>CT), RS1001368765 (2:176086070 T>A), RS1001502598 (2:176089221 T>C,G), RS1003168782 (2:176089153 A>G), RS1003221054 (2:176089545 G>A), RS1003284229 (2:176095995 G>A), RS1003422511 (2:176095630 G>A,C,T)

Disease associations

OMIM: gene MIM:142989 | disease phenotypes: MIM:610713, MIM:113200, MIM:113300, MIM:186000, MIM:186300, MIM:192350, MIM:603596

GenCC curated gene-disease

DiseaseClassificationInheritance
brachydactyly-syndactyly syndromeDefinitiveAutosomal dominant
synpolydactyly type 1StrongAutosomal dominant
syndactyly type 5StrongAutosomal dominant
brachydactyly type DStrongAutosomal dominant
brachydactyly type E1StrongAutosomal dominant
brachydactyly type ESupportiveAutosomal dominant

Mondo (15): brachydactyly-syndactyly syndrome (MONDO:0012544), brachydactyly type D (MONDO:0007222), brachydactyly type E1 (MONDO:0007223), synpolydactyly type 1 (MONDO:0008513), syndactyly type 5 (MONDO:0008516), brachydactyly type E (MONDO:0019677), VACTERL/vater association (MONDO:0008642), brachydactyly-syndactyly-oligodactyly syndrome (MONDO:0800344), skeletal dysplasia (MONDO:0018230), intellectual disability (MONDO:0001071), oligospermia (MONDO:0001913), male infertility (MONDO:0005372), syndactyly (MONDO:0021002), polydactyly (MONDO:0021003), synpolydactyly (MONDO:0021651)

Orphanet (9): Brachydactyly-syndactyly, Zhao type (Orphanet:93409), Synpolydactyly type 1 (Orphanet:295195), Brachydactyly type E (Orphanet:93387), Syndactyly type 5 (Orphanet:93406), VACTERL/VATER association (Orphanet:887), Primary bone dysplasia (Orphanet:364526), Syndactyly type 2 (Orphanet:93403), NON RARE IN EUROPE: Brachydactyly type D (Orphanet:93385), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

97 total (30 of 97 shown, HPO-id order):

HPOTerm
HP:0000003Multicystic kidney dysplasia
HP:0000006Autosomal dominant inheritance
HP:0000008Abnormal morphology of female internal genitalia
HP:0000028Cryptorchidism
HP:0000047Hypospadias
HP:0000048Bifid scrotum
HP:0000062Ambiguous genitalia
HP:0000086Ectopic kidney
HP:0000104Renal agenesis
HP:0000126Hydronephrosis
HP:0000175Cleft palate
HP:0000239Large fontanelles
HP:0000256Macrocephaly
HP:0000311Round face
HP:0000358Posteriorly rotated ears
HP:0000772Abnormal rib morphology
HP:0000776Congenital diaphragmatic hernia
HP:0000795Abnormality of the urethra
HP:0000894Short clavicles
HP:0001032Absent distal interphalangeal creases
HP:0001048Cavernous hemangioma
HP:0001156Brachydactyly
HP:0001159Syndactyly
HP:0001177Preaxial hand polydactyly
HP:0001195Single umbilical artery
HP:0001382Joint hypermobility
HP:0001440Metatarsal synostosis
HP:00015016 metacarpals
HP:0001511Intrauterine growth retardation
HP:0001539Omphalocele

GWAS associations

1 associations (top):

StudyTraitp-value
GCST006661_148Male-pattern baldness3.000000e-18

MeSH disease descriptors (10)

DescriptorNameTree numbers
D007248Infertility, MaleC12.100.500.430; C12.100.750.700; C12.200.294.430
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D009845OligospermiaC12.100.500.430.508; C12.100.750.700.508; C12.200.294.430.508
D017689PolydactylyC05.660.585.600; C16.131.621.585.600
D013576SyndactylyC05.116.099.370.894.819; C05.660.585.800; C05.660.906.819; C16.131.621.585.800; C16.131.621.906.819
C562420Brachydactyly, Type D (supp.)
C566194Brachydactyly, Type E (supp.)
C565193Brachydactyly-Syndactyly Syndrome (supp.)
C538153Syndactyly, type 2 (supp.)
C538155Syndactyly, type v (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

ChemicalActions (top 5)PubMed papers
(+)-JQ1 compounddecreases expression2
Valproic Acidincreases expression, increases methylation2
sodium arseniteincreases expression1
CGP 52608affects binding, increases reaction1
Resveratrolaffects cotreatment, decreases expression1
Benzo(a)pyreneincreases methylation, affects methylation1
Plant Extractsaffects cotreatment, decreases expression1
Vitalliumincreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_A3B1SEES3-1V human HOXD13, clone1Embryonic stem cellMale
CVCL_A3B2SEES3-1V human HOXD13, clone2Embryonic stem cellMale
CVCL_A3B3SEES3-1V human HOXD13, clone3Embryonic stem cellMale

Clinical trials (associated diseases)

299 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02307994PHASE4UNKNOWNClinical Research on Effectiveness and Safety of Treatment of Severe Oligospermia or Azoospermia With uFSH
NCT05320536PHASE4UNKNOWNA Clinical Study of Gulingji Capsule in the Treatment of Idiopathic Oligospermia, Asthenia, and Teratozoospermia
NCT06260007PHASE4RECRUITINGEfficacy and Safety Study of Products Based on Tribulus Terrestris, L. in Men With Oligospermia
NCT02202382PHASE4COMPLETEDEffects of Korean Red Ginseng on Male Infertility
NCT02204826PHASE4COMPLETEDEffects of Korean Red Ginseng on Semen Parameters in Male Infertility Patients: a Randomized, Placebo-controlled, Double-blind Clinical Study
NCT03802864PHASE4COMPLETEDPost-operative Pain Control of Testicular Sperm Extraction Using Liposomal Bupivacaine
NCT06100432PHASE4ACTIVE_NOT_RECRUITINGEffect of Eurycoma Longifolia (DLBS5055) and Multivitamins (Vitamin C+Vitamin E+ β-carotene) for Infertile Males
NCT07523022PHASE4ENROLLING_BY_INVITATIONComparison of the Effect of Gonadotropin and Clomiphene Citrate Treatment on Sperm Parameters and the Outcome of Assisted Reproductive Procedures in Subfertile Men Based on the APHRODITE Groups
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT00440180PHASE3TERMINATEDAromatase Inhibitors in the Treatment of Male Infertility
NCT00975117PHASE3COMPLETEDSpermotrend in the Treatment of Male Infertility
NCT01407432PHASE3COMPLETEDImpact of Folates in the Care of the Male Infertility
NCT01895816PHASE3COMPLETEDHerbal Tonic Fertile Supplement(ZO2C5)
NCT02605070PHASE3TERMINATEDPilot Study on the Effects of FSH Treatment on the Epigenetic Characteristics of Spermatozoa in Infertile Patients With Severe Oligozoospermia
NCT07402759PHASE3ACTIVE_NOT_RECRUITINGImpact of tdrd9 Gene Mutations in the Therapeutic Response to L-carnitine in Oligoasthenozoospermic Men
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT01409837PHASE2COMPLETEDThe Effect and Safety of Lisinopril in Non-hypertensive Men With Infertility From Low Sperm Count
NCT02234206PHASE2COMPLETEDA Clinical Trial to Study the Safety and Efficacy of Chandrakanthi Choornam in Patients With Low Sperm Count
NCT07481370PHASE2ENROLLING_BY_INVITATIONIsotretinoin vs hCG for Male Infertility Due to Low or Absent Sperm
NCT01880086PHASE2COMPLETEDClomiphene Citrate for the Treatment of Low Testosterone Associated With Chronic Opioid Pain Medication Administration
NCT02061384PHASE2COMPLETEDRA-2 13-cis Retinoic Acid (Isotretinoin)
NCT02421887PHASE2COMPLETEDMales, Antioxidants, and Infertility Trial
NCT05200663PHASE2UNKNOWNEfficacy Comparison of Tamoxifen and Tamoxifen With Antioxidants on Semen Quality of Male With Idiopathic Infertility
NCT05290558PHASE2ACTIVE_NOT_RECRUITINGThe Therapeutic Effects of Bu Shen Yi Jing Pill on Semen Quality in Sub Fertile Males: a Randomized Controlled Trial
NCT06091969PHASE2NOT_YET_RECRUITINGSupplementation for Male Subfertility
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT05158114PHASE1WITHDRAWNSafety of Cultured Allogeneic Adult Umbilical Cord Derived Mesenchymal Stem Cells for Testicular Injury and Oligospermia
NCT01595308PHASE1COMPLETEDA Pilot Study to Evaluate the Effect of Pomegranate Juice on Semen Parameters in Healthy Male Volunteers
NCT02122211PHASE1COMPLETEDCholine Dehydrogenase and Sperm Function: Effects of Betaine