HOXD3

Summary

HOXD3 (homeobox D3, HGNC:5137) is a protein-coding gene on chromosome 2q31.1, encoding Homeobox protein Hox-D3 (P31249). Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

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 at 2q31-2q37 chromosome regions. Deletions that removed the entire HOXD gene cluster or 5’ end of this cluster have been associated with severe limb and genital abnormalities. The protein encoded by this gene may play a role in the regulation of cell adhesion processes.

Source: NCBI Gene 3232 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 81 total
• Transcription factor: yes — 10 downstream targets (CollecTRI)
• MANE Select transcript: NM_006898

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:5137
Approved symbol	HOXD3
Name	homeobox D3
Location	2q31.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000128652
Ensembl biotype	protein_coding
OMIM	142980
Entrez	3232

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000249440, ENST00000410016, ENST00000432796, ENST00000459979, ENST00000683222, ENST00000873077, ENST00000873078, ENST00000873079, ENST00000963805

RefSeq mRNA: 1 — MANE Select: NM_006898 NM_006898

CCDS: CCDS2270

Canonical transcript exons

ENST00000683222 — 4 exons

Exon	Start	End
ENSE00003721456	176169031	176169655
ENSE00003917101	176171517	176173098
ENSE00003920502	176157307	176157452
ENSE00003921277	176164073	176164168

Expression profiles

Bgee: expression breadth ubiquitous, 169 present calls, max score 93.79.

FANTOM5 (CAGE): breadth broad, TPM avg 2.5311 / max 110.7015, expressed in 596 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
23857	1.2309	416
23858	0.3144	176
23867	0.2588	94
23859	0.2416	136
23856	0.2259	108
23855	0.1786	88
23854	0.0521	16
23866	0.0260	9
23869	0.0028	1

Top tissues by expression

283 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	93.79	gold quality
germinal epithelium of ovary	UBERON:0001304	85.59	gold quality
right uterine tube	UBERON:0001302	84.87	gold quality
body of uterus	UBERON:0009853	84.80	gold quality
seminal vesicle	UBERON:0000998	84.74	gold quality
cauda epididymis	UBERON:0004360	84.57	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.01	gold quality
caput epididymis	UBERON:0004358	83.51	gold quality
metanephros cortex	UBERON:0010533	83.41	gold quality
right ovary	UBERON:0002118	79.25	gold quality
sperm	CL:0000019	79.21	silver quality
left ovary	UBERON:0002119	79.14	gold quality
adult mammalian kidney	UBERON:0000082	78.69	gold quality
ovary	UBERON:0000992	78.26	gold quality
kidney	UBERON:0002113	77.99	gold quality
male germ cell	CL:0000015	76.79	silver quality
cortex of kidney	UBERON:0001225	76.75	gold quality
myometrium	UBERON:0001296	76.21	gold quality
stromal cell of endometrium	CL:0002255	76.19	gold quality
right adrenal gland cortex	UBERON:0035827	75.91	gold quality
metanephros	UBERON:0000081	75.10	gold quality
left uterine tube	UBERON:0001303	74.92	gold quality
left adrenal gland	UBERON:0001234	74.91	gold quality
left adrenal gland cortex	UBERON:0035825	74.52	gold quality
right adrenal gland	UBERON:0001233	74.51	gold quality
endocervix	UBERON:0000458	74.20	gold quality
adrenal tissue	UBERON:0018303	73.20	gold quality
adrenal gland	UBERON:0002369	73.01	gold quality
nephron tubule	UBERON:0001231	72.99	silver quality
hindlimb stylopod muscle	UBERON:0004252	72.82	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-119	yes	39.18
E-ANND-3	yes	3.12

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

10 targets.

Target	Regulation
GABRB3
ITGA3	Activation
ITGA5	Unknown
ITGAV	Unknown
ITGB1	Unknown
ITGB3	Unknown
MMP2	Activation
PLAU	Unknown
TTF1
WNT1

JASPAR motifs

Motif	Name	Family
MA0912.2	HOXD3	HOX

JASPAR matrix evidence (PMIDs): PMID:18585359

Upstream regulators (CollecTRI, top): EZH2, MYC

miRNA regulators (miRDB)

56 targeting HOXD3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-6856-5P	100.00	65.47	1298
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-1323	99.83	69.89	2471
HSA-MIR-4799-5P	99.82	70.60	2663
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-1283	99.69	72.42	3009
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-3120-3P	99.54	70.28	2669
HSA-MIR-203A-3P	99.49	70.56	2806
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4318	99.38	66.94	1505
HSA-MIR-5683	99.36	68.59	2083
HSA-MIR-190B-3P	99.33	68.29	1382
HSA-MIR-6739-3P	99.22	68.84	1843
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-29A-5P	99.08	68.59	1813
HSA-MIR-9898	99.00	67.89	500

Literature-anchored findings (GeneRIF, showing 21)

• transduction of antisense DNA into human melanoma cells results in decreased invasive and motile activities (PMID:12405287)
• Hox D3 coordinately regulates the expression of integrin alpha5beta1 and integrin alphavbeta3 during angiogenesis in vivo. (PMID:14610084)
• HoxD3 may provide a means to directly improve collagen deposition, angiogenesis and closure in poorly healing diabetic wounds. (PMID:14633614)
• HOXD3 may play an important role in regulating cerebral angiogenesis, and that gene transfer of HOXD3 may provide a novel and potent means to stimulate angiogenesis (PMID:15545924)
• The karyotype of our patient suggests another possible locus of the Duane syndrome, and the mapped genes around the deleted region, 1q42.13-43, contain possible candidate genes such as a homeobox gene. (PMID:17126050)
• Study identified hypermethylation and gene inactivation of HOXA4 and HOXA5 was frequently observed (26-79%) in all types of leukemias studied. (PMID:17785556)
• Further validation of candidate genes on a separate cohort of low and high grade prostate cancers by quantitative MethyLight analysis has allowed us to confirm DNA hypermethylation of HOXD3 and BMP7… (PMID:19283074)
• HOXD3 methylation distinguishes low-grade prostate cancers from intermediate and high-grade ones. (PMID:20212450)
• quantitative increase in promoter methylation levels of HOXD3 is associated with prostate cancer progression (PMID:21207416)
• High expression of HOXD3 correlates with invasive breast cancer. (PMID:22935821)
• describe familial cases of TH in two generations (proband and his father), in addition to other two sporadic cases. We have found polymorphisms in the HOXB3, HOXD3, and a new synonymous variant, and PITX2 genes (PMID:24127533)
• These results validate the association between promoter hypermethylation of ABHD9 and HOXD3 and prostate cancer recurrence (PMID:24718283)
• HOXD3 promoter hypermethylation is correlated with clinicopathologic features in prostate cancer. This correlation is more common in older, higher risk patients. (PMID:24847526)
• EGR1 is a key player in the transcriptional control of miR-203a, and that miR-203a acts as an anti-oncogene to suppress HCC tumorigenesis by targeting HOXD3 through EGFR-related cell signaling pathways. (PMID:27244890)
• the HOXD3 gene promotes colorectal cancer cell growth and plays a pivotal role in the development and survival of malignant human colorectal cancer cells. (PMID:27499213)
• The findings indicate that miR-203a inhibits hepatocellular carcinoma cell invasion, metastasis, and angiogenesis by negatively targeting HOXD3 and suppressing cell signaling through the VEGFR pathway. (PMID:29402992)
• Nuclear lncRNA HOXD-AS1 suppresses colorectal carcinoma growth and metastasis via inhibiting HOXD3-induced ITGB3 transcriptional activation and MAPK/AKT signaling. (PMID:30823921)
• HOXD3 was negatively regulated by YY1 recruiting HDAC1 to suppress progression of hepatocellular carcinoma cells via ITGA2 pathway. (PMID:32557953)
• HOXD3 Up-regulating KDM5C Promotes Malignant Progression of Diffuse Large B-Cell Lymphoma by Decreasing p53 Expression (PMID:34928233)
• Identification and validation of HOXD3 and UNC5C as molecular signatures in keloid based on weighted gene co-expression network analysis. (PMID:35709926)
• A pan-cancer analysis of the role of HOXD1, HOXD3, and HOXD4 and validation in renal cell carcinoma. (PMID:37827698)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	hoxd3a	ENSDARG00000059280
mus_musculus	Hoxd3	ENSMUSG00000079277
rattus_norvegicus	Hoxd3	ENSRNOG00000001577

Paralogs (42): HOXA11 (ENSG00000005073), HOXC8 (ENSG00000037965), HOXA1 (ENSG00000105991), HOXA2 (ENSG00000105996), HOXA3 (ENSG00000105997), HOXA5 (ENSG00000106004), HOXA6 (ENSG00000106006), HOXA13 (ENSG00000106031), TLX1 (ENSG00000107807), HOXB6 (ENSG00000108511), TLX2 (ENSG00000115297), HOXB8 (ENSG00000120068), HOXB5 (ENSG00000120075), HOXB3 (ENSG00000120093), HOXB1 (ENSG00000120094), HOXA7 (ENSG00000122592), HOXC13 (ENSG00000123364), HOXC11 (ENSG00000123388), HOXC12 (ENSG00000123407), HOXD1 (ENSG00000128645), HOXD9 (ENSG00000128709), HOXD10 (ENSG00000128710), HOXD11 (ENSG00000128713), HOXD13 (ENSG00000128714), PDX1 (ENSG00000139515), HOXB13 (ENSG00000159184), TLX3 (ENSG00000164438), HOXD4 (ENSG00000170166), HOXD12 (ENSG00000170178), HOXB9 (ENSG00000170689), HOXC5 (ENSG00000172789), HOXB2 (ENSG00000173917), HOXD8 (ENSG00000175879), GSX2 (ENSG00000180613), HOXC9 (ENSG00000180806), HOXC10 (ENSG00000180818), HOXB4 (ENSG00000182742), HOXA4 (ENSG00000197576), HOXC6 (ENSG00000197757), HOXC4 (ENSG00000198353)

Protein

Protein identifiers

Homeobox protein Hox-D3 — P31249 (reviewed: P31249)

Alternative names: Homeobox protein Hox-4A

All UniProt accessions (2): P31249, C9J1M3

UniProt curated annotations — full annotation on UniProt →

Function. Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Subcellular location. Nucleus.

Similarity. Belongs to the Antp homeobox family.

RefSeq proteins (1): NP_008829* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001356	HD	Domain
IPR001827	Homeobox_Antennapedia_CS	Conserved_site
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR017970	Homeobox_CS	Conserved_site
IPR020479	HD_metazoa	Domain
IPR025281	DUF4074	Domain

Pfam: PF00046, PF13293

UniProt features (12 total): region of interest 4, compositionally biased region 3, chain 1, DNA-binding region 1, sequence variant 1, sequence conflict 1, short sequence motif 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P31249-F1	58.01	0.16

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-5617472	Activation of anterior HOX genes in hindbrain development during early embryogenesis

MSigDB gene sets: 167 (showing top): BROWNE_HCMV_INFECTION_30MIN_DN, FXR_IR1_Q6, RRAGTTGT_UNKNOWN, GOBP_EMBRYO_DEVELOPMENT_ENDING_IN_BIRTH_OR_EGG_HATCHING, BENPORATH_ES_WITH_H3K27ME3, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GCANCTGNY_MYOD_Q6, GOBP_EMBRYONIC_SKELETAL_SYSTEM_DEVELOPMENT, TTTGTAG_MIR520D, GOBP_POSITIVE_REGULATION_OF_NEURON_DIFFERENTIATION, GOBP_EMBRYONIC_SKELETAL_SYSTEM_MORPHOGENESIS, GCAAGGA_MIR502, GOBP_NEUROGENESIS, GOBP_CRANIAL_NERVE_MORPHOGENESIS

GO Biological Process (13): DNA-templated transcription (GO:0006351), regulation of transcription by RNA polymerase II (GO:0006357), cell-matrix adhesion (GO:0007160), Notch signaling pathway (GO:0007219), anterior/posterior pattern specification (GO:0009952), positive regulation of gene expression (GO:0010628), glossopharyngeal nerve morphogenesis (GO:0021615), thyroid gland development (GO:0030878), positive regulation of neuron differentiation (GO:0045666), positive regulation of transcription by RNA polymerase II (GO:0045944), embryonic skeletal system morphogenesis (GO:0048704), cartilage development (GO:0051216), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (8): RNA polymerase II transcription regulatory region sequence-specific DNA binding (GO:0000977), RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677), DNA-binding transcription factor activity (GO:0003700), protein binding (GO:0005515)

GO Cellular Component (5): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), aggresome (GO:0016235), nuclear body (GO:0016604)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Activation of HOX genes during differentiation	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
RNA polymerase II transcription regulatory region sequence-specific DNA binding	3
gene expression	2
regulation of DNA-templated transcription	2
transcription by RNA polymerase II	2
regulation of gene expression	2
regulation of transcription by RNA polymerase II	2
transcription cis-regulatory region binding	2
cellular anatomical structure	2
RNA biosynthetic process	1
cell-substrate adhesion	1
cell surface receptor signaling pathway	1
regionalization	1
positive regulation of macromolecule biosynthetic process	1
glossopharyngeal nerve development	1
cranial nerve morphogenesis	1
endocrine system development	1
gland development	1
neuron differentiation	1
positive regulation of cell differentiation	1
regulation of neuron differentiation	1
positive regulation of DNA-templated transcription	1
embryonic organ morphogenesis	1
skeletal system morphogenesis	1
embryonic skeletal system development	1
skeletal system development	1
animal organ development	1
connective tissue development	1
DNA-templated transcription	1
regulation of RNA biosynthetic process	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
DNA-binding transcription factor activity, RNA polymerase II-specific	1
DNA-binding transcription activator activity	1
positive regulation of transcription by RNA polymerase II	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
transcription regulator activity	1
binding	1

Protein interactions and networks

STRING

894 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
HOXD3	MTX2	O75431	774
HOXD3	HOXD10	P28358	598
HOXD3	HOXD9	P28356	593
HOXD3	EDIL3	O43854	572
HOXD3	SHH	Q15465	530
HOXD3	CRIP3	Q6Q6R5	521
HOXD3	ITGB3	P05106	517
HOXD3	ITGA2B	P08514	502
HOXD3	TGFB2	P08112	439
HOXD3	TBX15	Q96SF7	429
HOXD3	PDZRN4	Q6ZMN7	414
HOXD3	HBZ	P02008	400
HOXD3	HOXD13	P35453	392
HOXD3	ALDH1A2	O94788	388
HOXD3	EVX2	Q03828	387

IntAct

24 interactions, top by confidence:

A	B	Type	Score
Hoxa1	HOXD3	psi-mi:“MI:0915”(physical association)	0.570
HOXD3	Hoxa1	psi-mi:“MI:0915”(physical association)	0.570
HOXD3	PRP39	psi-mi:“MI:0915”(physical association)	0.560
HOXD3	SMARCD1	psi-mi:“MI:0915”(physical association)	0.560
HOXD3	IGFN1	psi-mi:“MI:0915”(physical association)	0.560
HOXD3	NFKBID	psi-mi:“MI:0915”(physical association)	0.560
HOXD3	HOXC8	psi-mi:“MI:0915”(physical association)	0.560
HBZ	HOXD3	psi-mi:“MI:0915”(physical association)	0.490
HOXD3	HBZ	psi-mi:“MI:0915”(physical association)	0.490
DDB1	HOXD3	psi-mi:“MI:0915”(physical association)	0.370
HOXD3	ALX4	psi-mi:“MI:0915”(physical association)	0.370
HOXD3	GM2A	psi-mi:“MI:0914”(association)	0.350
NFKBID	HOXD3	psi-mi:“MI:0915”(physical association)	0.000
HOXC8	HOXD3	psi-mi:“MI:0915”(physical association)	0.000
SMARCD1	HOXD3	psi-mi:“MI:0915”(physical association)	0.000
IGFN1	HOXD3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (15): HOXD3 (PCA), Hoxa1 (Affinity Capture-Western), HOXD3 (Two-hybrid), HOXD3 (Two-hybrid), HOXD3 (Two-hybrid), IGFN1 (Two-hybrid), NFKBID (Two-hybrid), HOXD3 (Reconstituted Complex), SPRYD4 (Affinity Capture-MS), CTH (Affinity Capture-MS), GM2A (Affinity Capture-MS), HOXD3 (Affinity Capture-MS), HOXD3 (Two-hybrid), ALX4 (Two-hybrid), HOXD3 (Two-hybrid)

ESM2 similar proteins: A0A8V0YY16, A0JPN1, A1YG01, A2D4R4, A2D649, A2T6H5, A2T6Z0, A2T7J2, A3KNJ3, A7MB54, A8MTJ6, B5RHS5, D3Z120, O54743, P09027, P14653, P17919, P31249, P32183, P35584, P55316, P55318, P56260, Q00939, Q12946, Q12947, Q12948, Q12951, Q1A1A1, Q1A1A2, Q1A1A3, Q1A1A4, Q1A1A5, Q1A1A6, Q28D67, Q28HT3, Q3I5G5, Q3Y598, Q60987, Q61080

Diamond homologs: A1L2P5, A1YER7, A1YF08, A1YFD8, A1YFY3, A1YG85, A2D4P8, A2D5I1, A2D5K9, A2D5Y4, A2T6X6, A2T756, A8DT10, A9L937, B0VXK3, O13074, O42365, O42367, O42368, O42370, O43364, O43365, O57374, O93353, P02830, P02831, P06798, P09013, P09014, P09016, P09019, P09020, P09021, P09026, P09027, P09067, P09070, P09074, P09079, P09080

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
HOXD3	“up-regulates quantity by expression”	ITGA5	“transcriptional regulation”
HOXD3	“up-regulates quantity by expression”	“A5/b1 integrin”	“transcriptional regulation”
HMGB1	“up-regulates activity”	HOXD3	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

81 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	2
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1281 predictions. Top by Δscore:

Variant	Effect	Δscore
2:176152606:A:AG	acceptor_gain	1.0000
2:176152606:A:T	acceptor_loss	1.0000
2:176152606:AGT:A	acceptor_gain	1.0000
2:176152607:G:GG	acceptor_gain	1.0000
2:176152607:G:GT	acceptor_gain	1.0000
2:176152607:GT:G	acceptor_gain	1.0000
2:176152607:GTG:G	acceptor_gain	1.0000
2:176152607:GTGA:G	acceptor_gain	1.0000
2:176152607:GTGAA:G	acceptor_gain	1.0000
2:176152065:GG:G	donor_gain	0.9900
2:176152065:GGGT:G	donor_loss	0.9900
2:176152066:GG:G	donor_gain	0.9900
2:176152067:G:GC	donor_loss	0.9900
2:176152067:G:GG	donor_gain	0.9900
2:176152067:GT:G	donor_loss	0.9900
2:176152068:T:G	donor_loss	0.9900
2:176152598:T:TA	acceptor_gain	0.9900
2:176152603:C:A	acceptor_gain	0.9900
2:176152603:C:CA	acceptor_gain	0.9900
2:176161079:AGGT:A	donor_loss	0.9900
2:176161081:G:GC	donor_loss	0.9900
2:176161082:T:A	donor_loss	0.9900
2:176171510:T:A	acceptor_gain	0.9900
2:176171512:CCCA:C	acceptor_loss	0.9900
2:176171513:CCAG:C	acceptor_loss	0.9900
2:176171514:CA:C	acceptor_loss	0.9900
2:176171514:CAG:C	acceptor_loss	0.9900
2:176171515:A:AG	acceptor_gain	0.9900
2:176171515:A:C	acceptor_loss	0.9900
2:176171515:AG:A	acceptor_gain	0.9900

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000159751 (2:176157150 C>T), RS1000251570 (2:176170273 C>A), RS1000334284 (2:176150841 T>A), RS1000476286 (2:176152468 G>C), RS1000524728 (2:176171009 C>G), RS1000640863 (2:176157399 G>T), RS1001009929 (2:176162167 G>A,T), RS1001154091 (2:176171270 G>C,T), RS1001406560 (2:176157858 G>A), RS1001458945 (2:176158200 G>C,T), RS1001549747 (2:176164487 C>G,T), RS1001558569 (2:176163389 G>A,T), RS1001625388 (2:176152379 A>G), RS1001673214 (2:176156861 G>A), RS1001708480 (2:176164040 G>A)

Disease associations

OMIM: gene MIM:142980 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST000802_4	Ovarian cancer	5.000000e-14
GCST002967_2	Mucinous ovarian carcinoma	8.000000e-12
GCST002967_5	Mucinous ovarian carcinoma	8.000000e-07
GCST003225_16	Pelvic organ prolapse (moderate/severe)	9.000000e-06
GCST005051_8	Obstructive sleep apnea trait (apnea hypopnea index)	1.000000e-06
GCST005051_9	Obstructive sleep apnea trait (apnea hypopnea index)	4.000000e-07
GCST005116_16	Male-pattern baldness	1.000000e-14
GCST005116_17	Male-pattern baldness	3.000000e-13
GCST006661_148	Male-pattern baldness	3.000000e-18
GCST007876_9	Estimated glomerular filtration rate	1.000000e-14

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007817	sleep apnea measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

28 total (human), top 28 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance	2
Arsenic	increases abundance, decreases expression, affects cotreatment	2
titanium dioxide	increases methylation	1
arsenite	increases methylation	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
benazol P	affects expression	1
CGP 52608	increases reaction, affects binding	1
belinostat	increases expression	1
(+)-JQ1 compound	decreases expression	1
Decitabine	decreases methylation, increases expression	1
Vorinostat	increases expression	1
Amphotericin B	decreases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Catechin	increases expression	1
Flavonoids	increases expression	1
Indomethacin	decreases expression	1
Manganese	affects cotreatment, decreases expression, increases abundance	1
Nickel	decreases expression	1
Plant Extracts	increases expression	1
Silicon Dioxide	increases expression	1
Testosterone	decreases expression	1
Tretinoin	increases expression	1
Aflatoxin B1	decreases methylation	1
Sodium Selenite	increases expression	1
Antirheumatic Agents	increases expression	1
Cadmium Chloride	decreases expression	1
Magnetite Nanoparticles	increases methylation	1
Polyphenols	increases expression	1

Cellosaurus cell lines

3 cell lines: 3 embryonic stem cell

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_A3B4	SEES3-1V human HOXD3, clone1	Embryonic stem cell	Male
CVCL_A3B5	SEES3-1V human HOXD3, clone2	Embryonic stem cell	Male
CVCL_A3B6	SEES3-1V human HOXD3, clone3	Embryonic stem cell	Male

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.