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GeneE
10 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
β“˜GeneE is for informational purposes only. It is not a substitute for professional medical advice, diagnosis, or treatment.
HOXD13
homeobox D13
Chromosome 2 Β· 2q31.1
NCBI Gene: 3239Ensembl: ENSG00000128714.6HGNC: HGNC:5136UniProt: P35453
104PubMed Papers
27Diseases
0Drugs
32Pathogenic Variants
FUNCTIONAL ROLE
Transcription Factor
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
DNA-binding transcription activator activity, RNA polymerase II-specificsequence-specific double-stranded DNA bindingDNA bindingpositive regulation of transcription by RNA polymerase IIsynpolydactyly type 1syndactyly type 5brachydactyly-syndactyly syndromebrachydactyly type E1
✦AI Summary

HOXD13 is a sequence-specific transcription factor that plays critical roles in developmental regulation and disease pathogenesis. As a developmental regulator, HOXD13 functions in limb development, with pathogenic variants causing synpolydactyly type 1 (SPD1), characterized by webbed fingers and extra digits 1. The most common pathogenic variants are alanine repeat expansions, which correlate with phenotype severity 1. Mechanistically, disease-associated repeat expansions alter HOXD13's phase separation capacity and its ability to co-condense with transcriptional co-activators, leading to perturbation of transcriptional condensate composition and altered gene expression programs 2. Beyond developmental disorders, HOXD13 has emerged as a significant factor in cancer progression. In colorectal cancer, HOXD13 is upregulated and promotes immunosuppression by transcriptionally upregulating AREG and PILRA, leading to M2-type macrophage polarization and CD8+ T cell suppression 3. In gliomas, HOXD13 functions as a master regulator of IDH-mutant astrocytoma evolution, with treatment-associated epigenomic changes leading to HOXD13 activation 4. HOXD13 also plays a role in myelodysplastic syndromes, where NUP98-HOXD13 fusion proteins contribute to disease pathogenesis through effects on bone marrow mesenchymal stromal cells 5.

Sources cited
1
HOXD13 variants cause synpolydactyly type 1, with alanine repeat expansions being most common and correlating with phenotype severity
PMID: 37427568
2
Disease-associated repeat expansions alter HOXD13's phase separation capacity and transcriptional condensate composition
PMID: 32386547
3
HOXD13 promotes colorectal cancer immunosuppression by upregulating AREG and PILRA, leading to M2 macrophage polarization
PMID: 41735002
4
HOXD13 functions as a master regulator of IDH-mutant glioma evolution
PMID: 38117484
5
NUP98-HOXD13 fusion contributes to myelodysplastic syndrome pathogenesis through effects on bone marrow stromal cells
PMID: 39841001
Disease Associationsβ“˜27
synpolydactyly type 1Open Targets
0.79Strong
syndactyly type 5Open Targets
0.75Strong
brachydactyly-syndactyly syndromeOpen Targets
0.74Strong
brachydactyly type E1Open Targets
0.73Strong
Syndactyly type 2Open Targets
0.72Strong
brachydactyly type EOpen Targets
0.69Moderate
non-syndromic brachydactylyOpen Targets
0.68Moderate
VACTERL/vater associationOpen Targets
0.52Moderate
genetic disorderOpen Targets
0.50Moderate
brachydactyly-syndactyly-oligodactyly syndromeOpen Targets
0.50Moderate
polydactylyOpen Targets
0.46Moderate
zygodactyly type 3Open Targets
0.37Weak
skin basal cell carcinomaOpen Targets
0.37Weak
Endometrial Endometrioid AdenocarcinomaOpen Targets
0.37Weak
synpolydactylyOpen Targets
0.34Weak
syndactylyOpen Targets
0.34Weak
male infertilityOpen Targets
0.34Weak
Mesoaxial hand polydactylyOpen Targets
0.34Weak
oligospermiaOpen Targets
0.34Weak
Penile hypospadiasOpen Targets
0.34Weak
Brachydactyly DUniProt
Brachydactyly E1UniProt
Brachydactyly-syndactyly syndromeUniProt
Brachydactyly-syndactyly-oligodactyly syndromeUniProt
Syndactyly 5UniProt
Synpolydactyly 1UniProt
VACTERL associationUniProt
Pathogenic Variants32
NM_000523.4(HOXD13):c.183_203dup (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAla)Pathogenic
not provided|HOXD13-related disorder
β˜…β˜…β˜†β˜†2025β†’ Residue 71
NM_000523.4(HOXD13):c.916C>T (p.Arg306Trp)Pathogenic
Synpolydactyly type 1|Brachydactyly type E1|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 306
NM_000523.4(HOXD13):c.186_212dup (p.Ala63_Ala71dup)Pathogenic
not provided|HOXD13-related disorder|Syndactyly type 5
β˜…β˜…β˜†β˜†2024β†’ Residue 63
NM_000523.4(HOXD13):c.209_210insGGCTGCGGCGGCGGCAGCGGC (p.Ala65_Ala71dup)Pathogenic
Syndactyly type 5|Synpolydactyly type 1
β˜…β˜…β˜†β˜†2023β†’ Residue 65
NM_000523.4(HOXD13):c.212_213insGGCGGCTGCGGCGGCGGCAGCGGCAGC (p.Ala63_Ala71dup)Pathogenic
Synpolydactyly type 1|not provided
β˜…β˜…β˜†β˜†2021β†’ Residue 63
NM_000523.4(HOXD13):c.461C>A (p.Ser154Ter)Pathogenic
Inborn genetic diseases
β˜…β˜†β˜†β˜†2025β†’ Residue 154
NM_000523.4(HOXD13):c.663_664del (p.Glu221fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 221
NM_000523.4(HOXD13):c.212_213insTGCCGCCGCCGCAGCCGCCGCTGCCGC (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAlaAlaAla)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 71
NM_000523.4(HOXD13):c.206_207insAGCGGCGGCTGCGGCGGCGGCAGC (p.Ala71_Ser72insAlaAlaAlaAlaAlaAlaAlaAla)Pathogenic
not provided
β˜…β˜†β˜†β˜†2024β†’ Residue 71
NM_000523.4(HOXD13):c.684dup (p.Tyr229fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 229
NM_000523.4(HOXD13):c.938C>G (p.Thr313Arg)Likely pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 313
NM_000523.4(HOXD13):c.542_552del (p.Asn181fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 181
NM_000523.4(HOXD13):c.203_204insA (p.Ala69fs)Likely pathogenic
not provided|Brachydactyly-syndactyly syndrome
β˜…β˜†β˜†β˜†2021β†’ Residue 69
NM_000523.4(HOXD13):c.314_315del (p.Lys105fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 105
NM_000523.4(HOXD13):c.744_747del (p.Gln248fs)Pathogenic
Syndactyly type 5;Brachydactyly type E1;Synpolydactyly type 1;Brachydactyly type D
β˜…β˜†β˜†β˜†2017β†’ Residue 248
NM_000523.4(HOXD13):c.673del (p.Ser225fs)Pathogenic
Synpolydactyly type 1
β˜…β˜†β˜†β˜†β†’ Residue 225
NM_000523.4(HOXD13):c.708del (p.Asn236fs)Pathogenic
Synpolydactyly type 1
β˜…β˜†β˜†β˜†β†’ Residue 236
NM_000523.4(HOXD13):c.858del (p.Gln287fs)Pathogenic
HOXD13-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 287
NM_000523.4(HOXD13):c.979C>T (p.Arg327Ter)Likely pathogenic
HOXD13-related disorder
β˜†β˜†β˜†β˜†2024β†’ Residue 327
NM_000523.4(HOXD13):c.742C>T (p.Gln248Ter)Pathogenic
Synpolydactyly type 1
β˜†β˜†β˜†β˜†2016β†’ Residue 248
View on ClinVar β†—
Related Genes
PDCD1LG2Protein interaction100%SPDL1Protein interaction87%CD274Protein interaction82%SHHProtein interaction74%HOXD9Protein interaction72%HOXD10Protein interaction72%
Tissue Expression6 tissues
Brain
100%
Heart
0%
Lung
0%
Bone Marrow
0%
Ovary
0%
Liver
0%
Gene Interaction Network
Click a node to explore
HOXD13PDCD1LG2SPDL1CD274SHHHOXD9HOXD10
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P35453
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.96LoF Tolerant
pLIβ“˜
0.00Tolerant
Observed/Expected LoF0.63 [0.42–0.96]
RankingsWhere HOXD13 stands among ~20K protein-coding genes
  • #4,589of 20,598
    Most Researched104 Β· top quartile
  • #1,752of 5,498
    Most Pathogenic Variants32
  • #8,999of 17,882
    Most Constrained (LOEUF)0.96
Genes detectedHOXD13
Sources retrieved10 papers
Response timeβ€”
πŸ“„ Sources
10β–Ό
1
Unblending of Transcriptional Condensates in Human Repeat Expansion Disease.
PMID: 32386547
Cell Β· 2020
1.00
2
HOXD13-associated synpolydactyly: Extending and validating the genotypic and phenotypic spectrum with 38 new and 49 published families.
PMID: 37427568
Genet Med Β· 2023
0.90
3
Advancing drug development in myelodysplastic syndromes.
PMID: 39786387
Blood Adv Β· 2025
0.80
4
Genitourinary functions of Hoxa13 and Hoxd13.
PMID: 16002988
J Biochem Β· 2005
0.70
5
Human HOX gene mutations.
PMID: 11206481
Clin Genet Β· 2001
0.60