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    HOXD13 homeobox D13 [ Homo sapiens (human) ]

    Gene ID: 3239, updated on 9-Dec-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
    mouse all
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    Genomic context

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    See HOXD13 in Genome Data Viewer
    Location:
    2q31.1
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (176087487..176095944)
    RS_2024_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_000002.12Genomic 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. Novel mutations of the HOXD13 gene in hand and foot malformations. Nakano K, et al. Int Surg, 2007 Sep-Oct. PMID 18399101
    2. [Synpolydactyly in a Chinese kindred: mutation detection, prenatal ultrasonographic and molecular diagnosis]. Jin H, et al. Zhonghua Yi Xue Yi Chuan Xue Za Zhi, 2011 Dec. PMID 22161087
    3. Identification of a missense HOXD13 mutation in a Chinese family with syndactyly type I-c using exome sequencing. Deng H, et al. Mol Med Rep, 2017 Jul. PMID 28498426
    4. Deletions in HOXD13 segregate with an identical, novel foot malformation in two unrelated families. Goodman F, et al. Am J Hum Genet, 1998 Oct. PMID 9758628, Free PMC Article
    5. 2q31.1 microdeletion syndrome: redefining the associated clinical phenotype. Dimitrov B, et al. J Med Genet, 2011 Feb. PMID 21068127

    See all (101) 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
    		not available
    Brachydactyly type E1
    MedGen: C1862102 OMIM: 113300 GeneReviews: Not available
    		not available
    Brachydactyly-syndactyly syndrome
    MedGen: C1853137 OMIM: 610713 GeneReviews: Not available
    		not available
    Syndactyly type 5
    MedGen: C1861348 OMIM: 186300 GeneReviews: Not available
    		not available
    Synpolydactyly type 1
    MedGen: C5574994 OMIM: 186000 GeneReviews: Not available
    		not available

    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)

    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
    located_in 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_2024_08

    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

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

    Chemical Information
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