Gene Gene information from NCBI Gene database.
Entrez ID 3239
Gene name Homeobox D13
Gene symbol HOXD13
Synonyms (NCBI Gene)
BDEBDSDHOX4ISPDSPD1
Chromosome 2
Chromosome location 2q31.1
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 cluster
SNPs SNP information provided by dbSNP.
18
SNP ID Visualize variation Clinical significance Consequence
rs28928891 A>C,G Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs28928892 C>A,G Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs28933082 C>G,T Pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
rs104893635 A>G Pathogenic Coding sequence variant, missense variant, genic downstream transcript variant
rs121912541 G>A,C,T Pathogenic Intron variant, missense variant, coding sequence variant, genic downstream transcript variant
miRNA miRNA information provided by mirtarbase database.
71
miRTarBase ID miRNA Experiments Reference
MIRT027146 hsa-miR-103a-3p Sequencing 20371350
MIRT051222 hsa-miR-16-5p CLASH 23622248
MIRT047651 hsa-miR-10a-5p CLASH 23622248
MIRT045586 hsa-miR-149-5p CLASH 23622248
MIRT042641 hsa-miR-423-3p CLASH 23622248
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
42
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
GO:0000978 Function RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
142989 5136 ENSG00000128714
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
P35453
Protein name Homeobox protein Hox-D13 (Homeobox protein Hox-4I)
Protein function Sequence-specific transcription factor that binds gene promoters and activates their transcription (PubMed:24789103). Part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axi
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF12284 HoxA13_N 79 181 Hox protein A13 N terminal Family
PF00046 Homeodomain 277 333 Homeodomain Domain
Sequence
MSRAGSWDMDGLRADGGGAGGAPASSSSSSVAAAAASGQCRGFLSAPVFAGTHSGRAAAA
AAAAAAAAAAASGFAYPGTSERTGSSSSSSSSAVVAARPEAPPAKECPAPTPAAAAAAPP
SAPALGYGYHFGNGYYSCRMSHGVGLQQNALKSSPHASLGGFPVEKYMDVSGLASSSVPA
N
EVPARAKEVSFYQGYTSPYQHVPGYIDMVSTFGSGEPRHEAYISMEGYQSWTLANGWNS
QVYCTKDQPQGSHFWKSSFPGDVALNQPDMCVYRRGRKKRVPYTKLQLKELENEYAINKF
INKDKRRRISAATNLSERQVTIWFQNRRVKDKK
IVSKLKDTVS
Sequence length 343
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
42
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Brachydactyly type D Pathogenic; Likely pathogenic rs28928891, rs200750564, rs1574943406 RCV000015996
RCV002502445
RCV000850561
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brachydactyly type E Pathogenic rs28928891 RCV004562212
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brachydactyly type E1 Likely pathogenic; Pathogenic rs28933082, rs200750564, rs1574943406 RCV003450643
RCV002502445
RCV000850561
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Brachydactyly-syndactyly syndrome Likely pathogenic; Pathogenic rs771082552, rs878854346, rs200750564 RCV005414338
RCV000016003
RCV001253289
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Abnormal finger morphology Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ANEMIA CTD, Disgenet
CTD, Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ARTHRITIS, RHEUMATOID CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BRACHYDACTYLY Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
2-3 toe syndactyly Syndactyly Of The Toes BEFREE 17236141
★☆☆☆☆
Found in Text Mining only
2-3 toe syndactyly Syndactyly Of The Toes HPO_DG
★☆☆☆☆
Found in Text Mining only
Acute leukemia Leukemia BEFREE 15755899, 22643831, 25220590
★☆☆☆☆
Found in Text Mining only
Ambiguous Genitalia Ambiguous Genitalia HPO_DG
★☆☆☆☆
Found in Text Mining only
Anemia Anemia CTD_human_DG 27725143
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Anencephaly Anencephaly HPO_DG
★☆☆☆☆
Found in Text Mining only
Anus, Imperforate Imperforate anus HPO_DG
★☆☆☆☆
Found in Text Mining only
Anxiety Anxiety Disorder BEFREE 24857698
★☆☆☆☆
Found in Text Mining only
Anxiety Disorders Anxiety Disorder BEFREE 24857698
★☆☆☆☆
Found in Text Mining only
Arthritis, Psoriatic Psoriatic Arthritis BEFREE 28245522
★☆☆☆☆
Found in Text Mining only