Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
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

Show/Hide all (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
rs200750564	C>T	Likely-pathogenic, pathogenic, uncertain-significance	Coding sequence variant, genic downstream transcript variant, stop gained
rs536639583	G>C	Pathogenic, uncertain-significance	Intron variant, downstream transcript variant, missense variant, coding sequence variant, genic downstream transcript variant
rs749985629	CAA>-	Likely-pathogenic	Genic downstream transcript variant, inframe deletion, coding sequence variant
rs764838478	A>-	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs875989842	C>A	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs878854343	CAGCACCCACGCCT>-	Pathogenic	Genic downstream transcript variant, frameshift variant, coding sequence variant, intron variant
rs878854344	G>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs878854345	->GGCTGCGGCGGCGGCAGCGGC	Pathogenic	Genic downstream transcript variant, coding sequence variant, inframe insertion, intron variant
rs878854346	AGCGGCGGCTGCGGCGGCGGC>-,AGCGGCGGCTGCGGCGGCGGCAGCGGCGGCTGCGGCGGCGGC	Pathogenic	Coding sequence variant, intron variant, genic downstream transcript variant, inframe insertion, inframe deletion
rs878854400	C>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, stop gained, intron variant
rs879255265	G>A	Pathogenic	Coding sequence variant, missense variant, genic downstream transcript variant
rs886037831	G>A	Pathogenic	Splice donor variant, genic downstream transcript variant, intron variant
rs1574943406	GCCA>-	Pathogenic	Frameshift variant, genic downstream transcript variant, intron variant, coding sequence variant

Show/Hide all (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
MIRT052694	hsa-miR-1260b	CLASH	23622248
MIRT557014	hsa-miR-3936	PAR-CLIP	20371350
MIRT086201	hsa-miR-329-5p	PAR-CLIP	20371350
MIRT086205	hsa-miR-922	PAR-CLIP	20371350
MIRT086202	hsa-miR-488-5p	PAR-CLIP	20371350
MIRT086204	hsa-miR-298	PAR-CLIP	20371350
MIRT557013	hsa-miR-6721-5p	PAR-CLIP	20371350
MIRT299542	hsa-miR-92a-1-5p	PAR-CLIP	20371350
MIRT299543	hsa-miR-3147	PAR-CLIP	20371350
MIRT557012	hsa-miR-1303	PAR-CLIP	20371350
MIRT557014	hsa-miR-3936	PAR-CLIP	21572407
MIRT086212	hsa-miR-6783-5p	PAR-CLIP	21572407
MIRT086201	hsa-miR-329-5p	PAR-CLIP	21572407
MIRT086205	hsa-miR-922	PAR-CLIP	21572407
MIRT086202	hsa-miR-488-5p	PAR-CLIP	21572407
MIRT086204	hsa-miR-298	PAR-CLIP	21572407
MIRT086211	hsa-miR-6077	PAR-CLIP	21572407
MIRT557013	hsa-miR-6721-5p	PAR-CLIP	21572407
MIRT086207	hsa-miR-4271	PAR-CLIP	21572407
MIRT086209	hsa-miR-4725-3p	PAR-CLIP	21572407
MIRT086213	hsa-miR-6780b-5p	PAR-CLIP	21572407
MIRT299542	hsa-miR-92a-1-5p	PAR-CLIP	21572407
MIRT299543	hsa-miR-3147	PAR-CLIP	21572407
MIRT557012	hsa-miR-1303	PAR-CLIP	21572407
MIRT557014	hsa-miR-3936	PAR-CLIP	20371350
MIRT086201	hsa-miR-329-5p	PAR-CLIP	20371350
MIRT086205	hsa-miR-922	PAR-CLIP	20371350
MIRT086202	hsa-miR-488-5p	PAR-CLIP	20371350
MIRT086204	hsa-miR-298	PAR-CLIP	20371350
MIRT557013	hsa-miR-6721-5p	PAR-CLIP	20371350
MIRT299542	hsa-miR-92a-1-5p	PAR-CLIP	20371350
MIRT299543	hsa-miR-3147	PAR-CLIP	20371350
MIRT557012	hsa-miR-1303	PAR-CLIP	20371350
MIRT557014	hsa-miR-3936	PAR-CLIP	21572407
MIRT086212	hsa-miR-6783-5p	PAR-CLIP	21572407
MIRT086201	hsa-miR-329-5p	PAR-CLIP	21572407
MIRT086205	hsa-miR-922	PAR-CLIP	21572407
MIRT086202	hsa-miR-488-5p	PAR-CLIP	21572407
MIRT086204	hsa-miR-298	PAR-CLIP	21572407
MIRT086211	hsa-miR-6077	PAR-CLIP	21572407
MIRT557013	hsa-miR-6721-5p	PAR-CLIP	21572407
MIRT086207	hsa-miR-4271	PAR-CLIP	21572407
MIRT086209	hsa-miR-4725-3p	PAR-CLIP	21572407
MIRT086213	hsa-miR-6780b-5p	PAR-CLIP	21572407
MIRT299542	hsa-miR-92a-1-5p	PAR-CLIP	21572407
MIRT299543	hsa-miR-3147	PAR-CLIP	21572407
MIRT557012	hsa-miR-1303	PAR-CLIP	21572407
MIRT1053768	hsa-miR-1264	CLIP-seq
MIRT1053769	hsa-miR-1297	CLIP-seq
MIRT1053770	hsa-miR-26a	CLIP-seq
MIRT1053771	hsa-miR-26b	CLIP-seq
MIRT1053772	hsa-miR-3124-3p	CLIP-seq
MIRT1053773	hsa-miR-3201	CLIP-seq
MIRT1053774	hsa-miR-3940-5p	CLIP-seq
MIRT1053775	hsa-miR-4272	CLIP-seq
MIRT1053776	hsa-miR-4465	CLIP-seq
MIRT1053777	hsa-miR-4507	CLIP-seq
MIRT1053778	hsa-miR-4791	CLIP-seq
MIRT1053779	hsa-miR-548aa	CLIP-seq
MIRT1053780	hsa-miR-570	CLIP-seq
MIRT2012204	hsa-miR-511	CLIP-seq
MIRT2244586	hsa-miR-183	CLIP-seq
MIRT2244587	hsa-miR-4282	CLIP-seq
MIRT2244588	hsa-miR-4670-3p	CLIP-seq
MIRT2244589	hsa-miR-4719	CLIP-seq
MIRT2244590	hsa-miR-513b	CLIP-seq

Show/Hide all (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
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0000987	Function	Cis-regulatory region sequence-specific DNA binding	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IMP	24789103
GO:0001501	Process	Skeletal system development	IEA
GO:0001501	Process	Skeletal system development	TAS	8614804
GO:0003677	Function	DNA binding	IDA	26581570
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	8614804
GO:0003682	Function	Chromatin binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	IEA
GO:0003700	Function	DNA-binding transcription factor activity	ISS
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0006355	Process	Regulation of DNA-templated transcription	IEA
GO:0006355	Process	Regulation of DNA-templated transcription	TAS	9207113
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA
GO:0006366	Process	Transcription by RNA polymerase II	IEA
GO:0007389	Process	Pattern specification process	IEA
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0022612	Process	Gland morphogenesis	IEA
GO:0030326	Process	Embryonic limb morphogenesis	IEA
GO:0030539	Process	Male genitalia development	IEA
GO:0030850	Process	Prostate gland development	IEA
GO:0033574	Process	Response to testosterone	IEA
GO:0035108	Process	Limb morphogenesis	IEA
GO:0042127	Process	Regulation of cell population proliferation	IEA
GO:0042733	Process	Embryonic digit morphogenesis	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IMP	24789103
GO:0048619	Process	Embryonic hindgut morphogenesis	IEA
GO:0060527	Process	Prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis	IEA
GO:0060571	Process	Morphogenesis of an epithelial fold	IEA
GO:0060602	Process	Branch elongation of an epithelium	IEA
GO:0060687	Process	Regulation of branching involved in prostate gland morphogenesis	IEA
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IDA	28473536
GO:1990837	Function	Sequence-specific double-stranded DNA binding	IEA

MIM	HGNC	e!Ensembl
142989	5136	ENSG00000128714

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
NEVPARAKEVSFYQGYTSPYQHVPGYIDMVSTFGSGEPRHEAYISMEGYQSWTLANGWNS
QVYCTKDQPQGSHFWKSSFPGDVALNQPDMCVYRRGRKKRVPYTKLQLKELENEYAINKF
INKDKRRRISAATNLSERQVTIWFQNRRVKDKKIVSKLKDTVS

Sequence length

343

Interactions

View interactions

Show/Hide Causal Diseases (9)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Brachydactyly type D	Pathogenic; Likely pathogenic	rs28928891, rs200750564, rs1574943406	RCV000015996 RCV002502445 RCV000850561
Brachydactyly type E	Pathogenic	rs28928891	RCV004562212
Brachydactyly type E1	Likely pathogenic; Pathogenic	rs28933082, rs200750564, rs1574943406	RCV003450643 RCV002502445 RCV000850561
Brachydactyly-syndactyly syndrome	Likely pathogenic; Pathogenic	rs771082552, rs878854346, rs200750564	RCV005414338 RCV000016003 RCV001253289
Brachydactyly-syndactyly-oligodactyly syndrome	Pathogenic	rs875989842	RCV000210948
HOXD13-related disorder	Pathogenic	rs760539494, rs878854346	RCV004552132 RCV003479436
Syndactyly type 5	Pathogenic; Likely pathogenic	rs760539494, rs878854345, rs104893635, rs200750564, rs1574943406	RCV005868478 RCV000016001 RCV000016002 RCV002502445 RCV000850561
Synpolydactyly	Likely pathogenic; Pathogenic	rs200750564	RCV002259339
Synpolydactyly type 1	Pathogenic; Likely pathogenic	rs2105379203, rs878854400, rs879255265, rs886037831, rs121912541, rs28933082, rs878854343, rs878854344, rs764838478, rs878854345, rs200750564, rs1574943406, rs775525473	RCV001806412 RCV000210952 RCV000210949 RCV000210954 RCV000210946 RCV000210953 RCV000015993 RCV000015994 RCV000015999 RCV000016000 RCV001353047 RCV000016004 RCV001197466 RCV000850561 RCV000015992

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Abnormal finger morphology	Uncertain significance	rs1301927745	RCV001090181
Intellectual disability	Conflicting classifications of pathogenicity	rs767527649	RCV005626850
Skeletal dysplasia	Conflicting classifications of pathogenicity	rs748398268	RCV005626847
VATER association	Uncertain significance	rs587776824	RCV005414449

Show/Hide Text Mining Associations (67)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Astrocytoma	Associate	19488988
Ataxia	Associate	17236141
Brachydactyly	Associate	12649808, 17236141
Brachydactyly Syndactyly Syndrome	Associate	17236141
Brachydactyly Type D	Associate	12649808, 17236141
Brachydactyly Type E	Associate	22233338, 31283647
Breast Neoplasms	Associate	19488988, 26617782, 26617867, 26918343
Carcinogenesis	Associate	19488988
Carcinoma Hepatocellular	Associate	30506460
Carcinoma Hepatocellular	Stimulate	34910956
Carcinoma Non Small Cell Lung	Stimulate	35019173
Carcinoma Non Small Cell Lung	Inhibit	36341395
Celiac Disease	Associate	34220824
Cholangiocarcinoma	Associate	21876633
Cholangitis Sclerosing	Inhibit	32370568
Colitis Ulcerative	Associate	37273534
Colorectal Neoplasms	Associate	36160034
COVID 19	Associate	33173052
Daneman Davy Mancer syndrome	Associate	17236141
Erythema Infectiosum	Associate	23948678
Foot Deformities	Associate	18072967, 9758628
Glioblastoma	Associate	40209540
Glioma	Associate	35845958
Growth Disorders	Associate	30541462
Hand foot uterus syndrome	Associate	10364522
Hecht Scott syndrome	Associate	12382951, 17236141, 24789103
Hemangioblastoma	Associate	26768750
Hepatitis Autoimmune	Associate	32370568, 37102762
Hepatitis B	Associate	34910956
Hepatitis B Chronic	Associate	34910956
Hereditary pancreatitis	Associate	33423702
Hypospadias	Associate	9207113
Idiopathic Pulmonary Fibrosis	Associate	38226605
Inflammation	Associate	30506460, 34910956
Limb Deformities Congenital	Associate	30541462, 34159400, 35819063
Liver Cirrhosis	Associate	34910956
Liver Cirrhosis Biliary	Stimulate	37915081
Liver Diseases	Associate	34910956
Lung Injury	Associate	33173052
Lymphatic Metastasis	Inhibit	26617867
Melanoma	Associate	19488988
Mesomelia synostoses syndrome	Associate	31591517
Neoplasms	Associate	19488988, 26617782, 30807610, 35653119
Neoplasms	Inhibit	26617867
Neoplastic Syndromes Hereditary	Associate	33533119
Neuroblastoma	Associate	22879880
Nuchal Cord	Associate	28600059
Osteochondrodysplasias	Associate	30541462
Ovarian Neoplasms	Stimulate	36213580
Pancreatic Neoplasms	Associate	19488988, 24189220, 26617782
Pancreatic Neoplasms	Inhibit	26617867
Penoscrotal transposition	Associate	10364522
Polydactyly Postaxial	Associate	33533119
Polyps	Associate	33423702
Purpura Thrombocytopenic Idiopathic	Associate	29333980
Purpura Thrombocytopenic Idiopathic	Stimulate	31651870
Renal dysplasia limb defects syndrome	Associate	12382951
Sarcoma Ewing	Associate	35653119, 35921177
Squamous Cell Carcinoma of Head and Neck	Associate	28808656
Syndactyly	Associate	17236141, 21654727, 24789103, 28600059, 31870337, 33533119, 36195906
Syndactyly type 2	Associate	10364522, 12649808, 17236141, 18072967, 21814222, 23948678, 24789103, 31611522, 9207113, 9758628
Thyroid Cancer Papillary	Associate	24189220
Thyroid Neoplasms	Associate	24189220
Triphalangeal thumbs brachyectrodactyly	Associate	12382951
Uterine Cervical Neoplasms	Associate	19488988, 36833285
VACTERL association	Associate	34338422
VATER association	Associate	34338422

HOXD13 (homeobox D13)