HOXD13 (homeobox D13)

Gene

• Entrez ID: 3239
• Gene name: Homeobox D13
• Gene symbol: HOXD13
• Synonyms: BDE, BDSD, HOX4I, SPD, SPD1
• 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 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

miRNA

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

Gene ontology (GO)

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	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IBA	21873635
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	ISA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IMP	24789103
GO:0001501	Process	Skeletal system development	IEA
GO:0003677	Function	DNA binding	IDA	26581570
GO:0003682	Function	Chromatin binding	IEA
GO:0003700	Function	DNA-binding transcription factor activity	ISS
GO:0005654	Component	Nucleoplasm	IDA
GO:0006355	Process	Regulation of transcription, DNA-templated	TAS	9207113
GO:0006357	Process	Regulation of transcription by RNA polymerase II	IBA	21873635
GO:0007275	Process	Multicellular organism development	TAS	9207113
GO:0009952	Process	Anterior/posterior pattern specification	IEA
GO:0030539	Process	Male genitalia development	IEA
GO:0033574	Process	Response to testosterone	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	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

Other IDs

• MIM: 142989
• HGNC: 5136
• e!Ensembl: ENSG00000128714

Protein

• UniProt ID: 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

Associated diseases

Causal
Disease name	Disease term	dbSNP ID	References
Anemia	Anemia	rs118204044, rs118204045, rs118204046, rs121918330, rs869320719, rs869312029, rs121918332, rs869320724, rs767094129, rs786205058, rs786205059, rs137853119, rs137853120, rs137853121, rs1384933966, rs137853122, rs137853123, rs786205060, rs267607121, rs121908584, rs80338697, rs80338699, rs120074166, rs120074167, rs1050828, rs74575103, rs137852314, rs5030868, rs137852316, rs137852317, rs137852318, rs137852319, rs137852320, rs137852321, rs137852322, rs137852323, rs137852324, rs72554665, rs387906468, rs5030872, rs137852326, rs137852333, rs137852327, rs137852328, rs137852329, rs137852330, rs137852331, rs137852332, rs137852334, rs137852335, rs137852336, rs137852339, rs76645461, rs137852340, rs137852341, rs78478128, rs137852343, rs137852344, rs137852345, rs587776730, rs137852346, rs137852347, rs137852349, rs2070404412, rs2070350038, rs2070350009, rs137852303, rs137852304, rs33946267, rs34378160, rs33933298, rs11549407, rs35724775, rs34598529, rs41469945, rs267607201, rs80338694, rs80338696, rs387907018, rs398123546, rs78365220, rs587777100, rs587777101, rs483352840, rs869312752, rs765487627, rs1557229599, rs1557230040, rs1555524842, rs782090947, rs1358275550, rs1557229736, rs1557230573, rs1556323334, rs1233124208, rs1293528130, rs146864395, rs1595503440, rs1603411214, rs137852325, rs1575247302, rs1603411177, rs1336651679, rs782322505	27725143
Anencephaly	Anencephaly	rs773607884
Brachydactyly	BRACHYDACTYLY, TYPE D, Brachydactyly, Brachydactyly syndrome type E, Brachydactyly type E, NON RARE IN EUROPE: Brachydactyly type D	rs121908949, rs28937580, rs121909082, rs104894122, rs863223289, rs863223290, rs104894121, rs1587657302, rs863223292, rs74315386, rs74315387, rs28936397, rs753691079, rs121909348, rs121917852, rs121917853, rs121917854, rs121917855, rs121917859, rs121917861, rs267606873, rs267606872, rs267606985, rs267606986, rs267606987, rs267606988, rs28933082, rs397514519, rs869025613, rs869025614, rs886039878, rs1553540620, rs1057518333, rs1948841937, rs1948868228, rs1948842030, rs1948842142	24239177, 12649808, 17236141, 12649808
Brachydactyly-syndactyly syndrome	BRACHYDACTYLY-SYNDACTYLY SYNDROME, Brachydactyly-syndactyly, Zhao type	rs878854346, rs200750564	24239177, 23995701, 17236141, 12649808
Brachydactyly-syndactyly-oligodactyly syndrome	BRACHYDACTYLY-SYNDACTYLY-OLIGODACTYLY SYNDROME	rs875989842	17236141
Congenital diaphragmatic hernia	Congenital diaphragmatic hernia	rs121908602, rs121908604, rs864309713, rs780263938, rs756636036, rs775394591
Cryptorchidism	Cryptorchidism	rs121912555, rs104894697, rs104894698, rs398122886
Macrocephaly	Macrocephaly	rs786204854, rs764333096, rs1557739557
Neutropenia	Neutropenia	rs879253882	27725143
Oligospermia	Oligospermia	rs1602125411, rs2047796277, rs377712900
Polydactyly	Polydactyly, Polydactyly preaxial type 1	rs1583729398, rs121917709, rs1583734240, rs121917714, rs397507422, rs398122899, rs587776959, rs386833752, rs1057518698, rs1060499558, rs755938967, rs1375768446, rs1309855392, rs1565601979, rs748321474, rs368652620, rs1562587032, rs760694987	17236141
Polysyndactyly	Polysyndactyly	rs1583729562, rs121917713
Rheumatoid arthritis	Rheumatoid Arthritis	rs3766379, rs3792876, rs2071592, rs3087456, rs587776843, rs1566328963, rs2240340, rs1557787212	17568789
Syndactyly	Syndactyly, Syndactyly, type v, Syndactyly, type 2	rs878854345, rs104893635, rs28931600, rs587777050, rs587777051, rs606231304	17236141, 12649808, 24239177, 26581570, 24789103, 12649808, 8817328, 24239177, 16222680, 22448207, 12414828, 17236141
Synpolydactyly	Synpolydactyly type 1	rs878854343, rs878854344, rs764838478, rs28933082, rs878854345, rs121912541, rs878854400, rs879255265, rs886037831, rs200750564
Vacterl association	VACTERL Association, VACTERL/VATER association, VATER Association, VATER/VACTERL ASSOCIATION	rs752504125, rs869320684, rs776556963	19006232, 12649808

Unknown
Disease name	Disease term	dbSNP ID	References
Abnormal spinal segmentation	Defect of vertebral segmentation
Ambiguous genitalia	Ambiguous Genitalia	rs782562963
Camptodactyly of fingers	Clinodactyly of the 5th finger
Carpal synostosis	Carpal synostosis
Congenital anomaly of limb	Limb Deformities, Congenital		8620844
Congenital camptodactyly	Congenital Camptodactyly
Short clavicles	Congenital hypoplasia of clavicle
Congenital hypoplasia of penis	Congenital hypoplasia of penis
Congenital omphalocele	Congenital omphalocele
Dwarfism	Dwarfism
Ectopic kidney	Ectopic kidney
Foot polydactyly	Postaxial foot polydactyly
Frontal bossing	Frontal bossing
Congenital gallbladder anomaly	Gallbladder anomaly congenital
Heart septal defects	Heart Septal Defects
Hemangioma, cavernous	Hemangioma, Cavernous
Hydronephrosis	Hydronephrosis
Hypospadias	Hypospadias
Imperforate anus	Anus, Imperforate
Laryngomalacia	Laryngomalacia
Lymphopenia	Lymphopenia		27725143
Multicystic renal dysplasia	Multicystic Dysplastic Kidney
Occipital encephalocele	Occipital Encephalocele
Oligodactyly	Oligodactyly
Penile hypospadias	Penile hypospadias
Renal agenesis	Congenital absence of kidneys syndrome
Syndactyly of fingers	Syndactyly of fingers, Cutaneous finger syndactyly
Syndactyly of the toes	Syndactyly of the toes, 2-3 toe syndactyly
Tracheal stenosis	Tracheal Stenosis
Zygodactyly	Zygodactyly type 3