BMP3
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Summary
BMP3 (bone morphogenetic protein 3, HGNC:1070) is a protein-coding gene on chromosome 4q21.21, encoding Bone morphogenetic protein 3 (P12645). Growth factor of the TGF-beta superfamily that plays an essential role in developmental process by inducing and patterning early skeletal formation and by negatively regulating bone density.
This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. Ligands of this family bind various TGF-beta receptors leading to recruitment and activation of SMAD family transcription factors that regulate gene expression. The encoded preproprotein is proteolytically processed to generate each subunit of the disulfide-linked homodimer. This protein suppresses osteoblast differentiation, and negatively regulates bone density, by modulating TGF-beta receptor availability to other ligands.
Source: NCBI Gene 651 — RefSeq curated summary.
At a glance
- Gene–disease (curated): coloboma (Moderate, GenCC)
- GWAS associations: 12
- Clinical variants (ClinVar): 83 total
- MANE Select transcript:
NM_001201
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:1070 |
| Approved symbol | BMP3 |
| Name | bone morphogenetic protein 3 |
| Location | 4q21.21 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000152785 |
| Ensembl biotype | protein_coding |
| OMIM | 112263 |
| Entrez | 651 |
Gene structure
Transcript identifiers
Ensembl transcripts: 2 — 2 protein_coding
ENST00000282701, ENST00000909109
RefSeq mRNA: 1 — MANE Select: NM_001201
NM_001201
CCDS: CCDS3588
Canonical transcript exons
ENST00000282701 — 3 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001007113 | 81030708 | 81031600 |
| ENSE00001007115 | 81045738 | 81046648 |
| ENSE00001549055 | 81053345 | 81057627 |
Expression profiles
Bgee: expression breadth ubiquitous, 126 present calls, max score 79.85.
FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.4027 / max 28.5608, expressed in 129 samples.
FANTOM5 promoters (3 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 48540 | 0.1753 | 71 |
| 48539 | 0.1668 | 69 |
| 48538 | 0.0606 | 25 |
Top tissues by expression
275 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| muscle layer of sigmoid colon | UBERON:0035805 | 79.85 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 79.20 | gold quality |
| rectum | UBERON:0001052 | 77.84 | gold quality |
| transverse colon | UBERON:0001157 | 76.66 | gold quality |
| mucosa of transverse colon | UBERON:0004991 | 74.15 | gold quality |
| sigmoid colon | UBERON:0001159 | 73.32 | gold quality |
| colon | UBERON:0001155 | 73.07 | gold quality |
| lower esophagus muscularis layer | UBERON:0035833 | 72.57 | gold quality |
| lower esophagus | UBERON:0013473 | 72.41 | gold quality |
| large intestine | UBERON:0000059 | 72.16 | gold quality |
| intestine | UBERON:0000160 | 71.39 | gold quality |
| tibial nerve | UBERON:0001323 | 70.93 | gold quality |
| small intestine Peyer’s patch | UBERON:0003454 | 70.61 | gold quality |
| esophagogastric junction muscularis propria | UBERON:0035841 | 69.25 | gold quality |
| small intestine | UBERON:0002108 | 68.96 | gold quality |
| olfactory segment of nasal mucosa | UBERON:0005386 | 67.82 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 67.08 | silver quality |
| gall bladder | UBERON:0002110 | 65.41 | gold quality |
| colonic epithelium | UBERON:0000397 | 64.85 | gold quality |
| ileal mucosa | UBERON:0000331 | 62.47 | silver quality |
| cortical plate | UBERON:0005343 | 61.54 | gold quality |
| right uterine tube | UBERON:0001302 | 61.28 | gold quality |
| pancreatic ductal cell | CL:0002079 | 59.81 | silver quality |
| duodenum | UBERON:0002114 | 59.68 | gold quality |
| ganglionic eminence | UBERON:0004023 | 59.33 | gold quality |
| minor salivary gland | UBERON:0001830 | 58.63 | gold quality |
| urinary bladder | UBERON:0001255 | 58.46 | gold quality |
| bone marrow cell | CL:0002092 | 58.09 | silver quality |
| left ovary | UBERON:0002119 | 56.65 | gold quality |
| decidua | UBERON:0002450 | 56.55 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 11.52 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
222 targeting BMP3, 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-190A-3P | 100.00 | 80.35 | 5520 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-6876-5P | 100.00 | 67.68 | 2126 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-4476 | 100.00 | 68.18 | 2030 |
| HSA-MIR-4795-3P | 100.00 | 74.62 | 4024 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-126-5P | 100.00 | 72.71 | 3180 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-3613-3P | 100.00 | 76.36 | 7965 |
| HSA-MIR-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-4776-3P | 100.00 | 68.73 | 1340 |
| HSA-MIR-8485 | 100.00 | 77.57 | 4731 |
| HSA-MIR-34A-5P | 99.99 | 71.21 | 1784 |
| HSA-MIR-449A | 99.99 | 71.05 | 1776 |
| HSA-MIR-548AW | 99.99 | 72.57 | 3559 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-181A-5P | 99.99 | 72.96 | 2995 |
| HSA-MIR-181B-5P | 99.99 | 72.97 | 2996 |
| HSA-MIR-181C-5P | 99.99 | 72.95 | 2996 |
| HSA-MIR-181D-5P | 99.99 | 73.04 | 2997 |
| HSA-MIR-4789-3P | 99.99 | 70.75 | 2484 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
Literature-anchored findings (GeneRIF, showing 19)
- The expression signals of BMP3 mRNA in malignant schwannoma were relatively lower than in benign lesions (PMID:11642720)
- BMP-3 receptor specificity is controlled by the interaction of Lys-30 of BMP-3 with Glu-76 of ActRIIb (PMID:17924656)
- BMP3 silencing is an early and frequent event in colorectal tumors progressing via the serrated and traditional pathways. (PMID:18311777)
- These results demonstrate that BMP-3 stimulates mesenchymal stem cell proliferation via the TGF-beta/activin signaling pathway. (PMID:20143330)
- Data suggest that promotor region methylation of the BMP3 gene may cause gastric carcinoma in Chinese people. (PMID:20238409)
- Features supportive of positive selection in the BMP3 gene were found including the presence of an excess of nonsynonymous mutations in modern humans, and a significantly lower genetic diversity that deviates from neutrality (PMID:20532035)
- Circulating bone morphogenetic protein 1-3 isoform increases renal fibrosis. (PMID:21415150)
- a critical link between HNF1A-MODY-induced alterations in Bmp-3 expression and insulin gene levels (PMID:21628466)
- As an addition to PRKG2 and RASGEFIB genes, we propose to include BMP3 gene as the principal determinant of the observed common phenotype. (PMID:22303795)
- Bone morphogenic protein 3 signaling in the regulation of osteogenesis. (PMID:23127436)
- Methylation level in stool decreases dramatically following colorectal cancer resection (PMID:24993691)
- BMP3 - the biomarker of a currently in-use multi-target stool DNA test was commonly expressed in tumor tissue specimens, independent of Fecal Immunochemical Test result. (PMID:28044229)
- a novel microRNA miR-450b was essential for adipose-derived mesenchymal stem cell differentiation, which could promote osteogenic differentiation in vitro and enhance bone formation in vivo by directly suppressing BMP3. (PMID:29649414)
- This study demonstrated that there was a significantly higher frequency of BMP3 methylated DNA in plasma in patients with polyps versus healthy controls with a sensitivity and specificity of 40 and 94%, respectively. (PMID:29892846)
- Results found that BMP3 gene was extensively hypermethylated and downregulated in colorectal cancer (CRC) and suggest that BMP3 acts as a tumor suppressor or has a growth rate-limiting role in CRC development and progression. (PMID:31665064)
- Inhibition of BMP3 increases the inflammatory response of fibroblast-like synoviocytes in rheumatoid arthritis. (PMID:32568738)
- USF2 reduces BMP3 expression via transcriptional activation of miR-34a, thus promoting osteogenic differentiation of BMSCs. (PMID:34350522)
- LncRNA SNHG3 regulates the BMSC osteogenic differentiation in bone metastasis of breast cancer by modulating the miR-1273g-3p/BMP3 axis. (PMID:35081500)
- Overexpression of lncRNA A2M-AS1 inhibits cell growth and aggressiveness via regulating the miR-587/bone morphogenetic protein 3 axis in lung adenocarcinoma. (PMID:36461613)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | bmp3 | ENSDARG00000060526 |
| mus_musculus | Bmp3 | ENSMUSG00000029335 |
| rattus_norvegicus | Bmp3 | ENSRNOG00000002381 |
Paralogs (31): TGFB2 (ENSG00000092969), BMP7 (ENSG00000101144), TGFB1 (ENSG00000105329), BMP5 (ENSG00000112175), BMP8B (ENSG00000116985), TGFB3 (ENSG00000119699), INHBA (ENSG00000122641), INHA (ENSG00000123999), BMP4 (ENSG00000125378), BMP2 (ENSG00000125845), GDF5 (ENSG00000125965), GDF1 (ENSG00000130283), BMP15 (ENSG00000130385), GDF15 (ENSG00000130513), GDF11 (ENSG00000135414), MSTN (ENSG00000138379), INHBE (ENSG00000139269), LEFTY2 (ENSG00000143768), GDF7 (ENSG00000143869), BMP6 (ENSG00000153162), GDF6 (ENSG00000156466), NODAL (ENSG00000156574), INHBB (ENSG00000163083), BMP10 (ENSG00000163217), GDF9 (ENSG00000164404), INHBC (ENSG00000175189), BMP8A (ENSG00000183682), GDF3 (ENSG00000184344), LEFTY1 (ENSG00000243709), GDF2 (ENSG00000263761), GDF10 (ENSG00000266524)
Protein
Protein identifiers
Bone morphogenetic protein 3 — P12645 (reviewed: P12645)
Alternative names: Bone morphogenetic protein 3A, Osteogenin
All UniProt accessions (1): P12645
UniProt curated annotations — full annotation on UniProt →
Function. Growth factor of the TGF-beta superfamily that plays an essential role in developmental process by inducing and patterning early skeletal formation and by negatively regulating bone density. Antagonizes the ability of certain osteogenic BMPs to induce osteoprogenitor differentiation and ossification. Initiates signaling cascades by associating with type II receptor ACVR2B to activate SMAD2-dependent and SMAD-independent signaling cascades including TAK1 and JNK pathways.
Subunit / interactions. Homodimer; disulfide-linked. Interacts with type II receptor ACVR2B.
Subcellular location. Secreted.
Tissue specificity. Expressed in adult and fetal cartilage.
Induction. Highly expressed in fracture tissue, particularly in osteoblasts, osteoclasts and chondroblasts.
Similarity. Belongs to the TGF-beta family.
RefSeq proteins (1): NP_001192* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001839 | TGF-b_C | Domain |
| IPR015615 | TGF-beta-like | Family |
| IPR017197 | BMP3/BMP3B | Family |
| IPR017948 | TGFb_CS | Conserved_site |
| IPR029034 | Cystine-knot_cytokine | Homologous_superfamily |
Pfam: PF00019
UniProt features (34 total): strand 9, glycosylation site 5, sequence variant 5, disulfide bond 4, turn 2, helix 2, region of interest 2, compositionally biased region 2, signal peptide 1, propeptide 1, chain 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 2QCQ | X-RAY DIFFRACTION | 2.21 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-P12645-F1 | 65.11 | 0.24 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Disulfide bonds (4): 370–437, 399–469, 403–471, 436
Glycosylation sites (5): 220, 463, 117, 141, 175
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 143 (showing top):
RNGTGGGC_UNKNOWN, GOBP_CARTILAGE_DEVELOPMENT, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOBP_OSTEOBLAST_DIFFERENTIATION, GOMF_GROWTH_FACTOR_ACTIVITY, GOBP_CELL_CELL_SIGNALING, GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS, SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_OSSIFICATION, GOMF_CYTOKINE_ACTIVITY, SABATES_COLORECTAL_ADENOMA_DN, GOBP_CONNECTIVE_TISSUE_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_OSSIFICATION, GOMF_SIGNALING_RECEPTOR_BINDING
GO Biological Process (9): skeletal system development (GO:0001501), osteoblast differentiation (GO:0001649), cell surface receptor protein serine/threonine kinase signaling pathway (GO:0007178), cell-cell signaling (GO:0007267), negative regulation of ossification (GO:0030279), positive regulation of transcription by RNA polymerase II (GO:0045944), cartilage development (GO:0051216), ossification (GO:0001503), cell differentiation (GO:0030154)
GO Molecular Function (4): signaling receptor binding (GO:0005102), cytokine activity (GO:0005125), growth factor activity (GO:0008083), BMP receptor binding (GO:0070700)
GO Cellular Component (3): obsolete extracellular space (GO:0005615), extracellular exosome (GO:0070062), extracellular region (GO:0005576)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| ossification | 2 |
| receptor ligand activity | 2 |
| system development | 1 |
| cell differentiation | 1 |
| enzyme-linked receptor protein signaling pathway | 1 |
| cell communication | 1 |
| signaling | 1 |
| regulation of ossification | 1 |
| negative regulation of multicellular organismal process | 1 |
| regulation of transcription by RNA polymerase II | 1 |
| transcription by RNA polymerase II | 1 |
| positive regulation of DNA-templated transcription | 1 |
| skeletal system development | 1 |
| animal organ development | 1 |
| connective tissue development | 1 |
| multicellular organismal process | 1 |
| cellular developmental process | 1 |
| protein binding | 1 |
| transmembrane receptor protein serine/threonine kinase binding | 1 |
| extracellular vesicle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
1278 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| BMP3 | ACVR2B | Q13705 | 887 |
| BMP3 | NDRG4 | Q9ULP0 | 840 |
| BMP3 | AMBN | Q9NP70 | 779 |
| BMP3 | ACVR2A | P27037 | 726 |
| BMP3 | TFPI2 | P48307 | 695 |
| BMP3 | BMPR1B | P78366 | 691 |
| BMP3 | IBSP | P21815 | 677 |
| BMP3 | BMPR1A | P36894 | 670 |
| BMP3 | BMPR2 | Q13873 | 635 |
| BMP3 | SMAD4 | Q13485 | 626 |
| BMP3 | SEPTIN9 | Q9UHD8 | 620 |
| BMP3 | BMP1 | P13497 | 615 |
| BMP3 | SPP1 | P10451 | 609 |
| BMP3 | VIM | P08670 | 575 |
| BMP3 | FST | P19883 | 574 |
IntAct
6 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| BMP3 | WFIKKN1 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| BMP3 | WFIKKN2 | psi-mi:“MI:0407”(direct interaction) | 0.440 |
| BMP2K | BMP3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| BMP3 | KDM1A | psi-mi:“MI:0915”(physical association) | 0.370 |
| BMP3 | PRMT6 | psi-mi:“MI:0915”(physical association) | 0.370 |
BioGRID (4): BMP3 (Affinity Capture-MS), YBX3 (Cross-Linking-MS (XL-MS)), KDM1A (Two-hybrid), PRMT6 (Two-hybrid)
ESM2 similar proteins: A2VDJ0, A9CB18, O13048, O18752, O18753, O60383, O70183, O77681, O95813, O95972, P09529, P12645, P14082, P17491, P20722, P21237, P22003, P22004, P22444, P23363, P25429, P27093, P49002, P49003, Q04906, Q04999, Q07105, Q08DV9, Q0EAB7, Q28GB8, Q3SAT7, Q3U3D7, Q66NC0, Q6PX77, Q7T2X6, Q7T2X7, Q7YRB4, Q800B9, Q8BHE5, Q8QG74
Diamond homologs: A1C2U3, A1C2U6, A1C2U7, A1C2V0, A1C2V5, A8E7N9, G5EEL5, O08689, O14793, O18828, O18830, O18831, O18836, O35312, O42220, O42221, O42222, O46576, O61643, O95390, O95393, P09534, P12644, P12645, P17491, P18075, P20722, P20863, P22003, P22004, P22444, P23359, P27091, P27539, P35621, P43026, P43027, P43028, P43029, P48970
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
83 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 72 |
| Likely benign | 2 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
476 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 4:81045733:CCTAG:C | acceptor_loss | 1.0000 |
| 4:81045734:CTA:C | acceptor_loss | 1.0000 |
| 4:81045735:TAG:T | acceptor_loss | 1.0000 |
| 4:81045736:A:AG | acceptor_gain | 1.0000 |
| 4:81045736:A:T | acceptor_loss | 1.0000 |
| 4:81045737:G:GG | acceptor_gain | 1.0000 |
| 4:81045737:GAA:G | acceptor_gain | 1.0000 |
| 4:81045737:GAAA:G | acceptor_gain | 1.0000 |
| 4:81031597:GCAG:G | donor_gain | 0.9900 |
| 4:81031598:CAG:C | donor_loss | 0.9900 |
| 4:81031599:AGG:A | donor_loss | 0.9900 |
| 4:81031600:GGTG:G | donor_loss | 0.9900 |
| 4:81045737:GA:G | acceptor_gain | 0.9900 |
| 4:81045737:GAAAC:G | acceptor_gain | 0.9900 |
| 4:81053453:A:AG | donor_gain | 0.9900 |
| 4:81053454:G:GG | donor_gain | 0.9900 |
| 4:81031603:GAGT:G | donor_loss | 0.9800 |
| 4:81031601:G:GG | donor_gain | 0.9600 |
| 4:81045735:TAGAA:T | acceptor_gain | 0.9600 |
| 4:81045736:AGAAA:A | acceptor_gain | 0.9600 |
| 4:81053343:A:AG | acceptor_gain | 0.9600 |
| 4:81053344:G:GG | acceptor_gain | 0.9600 |
| 4:81045734:CTAG:C | acceptor_gain | 0.9500 |
| 4:81045733:CCTA:C | acceptor_gain | 0.9300 |
| 4:81045732:TCCTA:T | acceptor_gain | 0.9200 |
| 4:81045737:G:T | acceptor_gain | 0.9100 |
| 4:81045739:A:AG | acceptor_gain | 0.9000 |
| 4:81045740:A:G | acceptor_gain | 0.8700 |
| 4:81046497:C:T | donor_gain | 0.8700 |
| 4:81053484:T:TA | donor_gain | 0.8700 |
AlphaMissense
3083 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 4:81046618:C:G | C399W | 1.000 |
| 4:81046545:T:C | L375P | 0.999 |
| 4:81046556:T:C | F379L | 0.999 |
| 4:81046557:T:G | F379C | 0.999 |
| 4:81046558:T:A | F379L | 0.999 |
| 4:81046558:T:G | F379L | 0.999 |
| 4:81046573:G:C | W384C | 0.999 |
| 4:81046573:G:T | W384C | 0.999 |
| 4:81046616:T:A | C399S | 0.999 |
| 4:81046616:T:C | C399R | 0.999 |
| 4:81046617:G:A | C399Y | 0.999 |
| 4:81046617:G:C | C399S | 0.999 |
| 4:81046628:T:C | C403R | 0.999 |
| 4:81046629:G:A | C403Y | 0.999 |
| 4:81046634:T:C | F405L | 0.999 |
| 4:81046635:T:G | F405C | 0.999 |
| 4:81046636:C:A | F405L | 0.999 |
| 4:81046636:C:G | F405L | 0.999 |
| 4:81053426:T:A | C437S | 0.999 |
| 4:81053426:T:C | C437R | 0.999 |
| 4:81053427:G:A | C437Y | 0.999 |
| 4:81053427:G:C | C437S | 0.999 |
| 4:81053428:T:G | C437W | 0.999 |
| 4:81053523:G:A | C469Y | 0.999 |
| 4:81053524:C:G | C469W | 0.999 |
| 4:81053528:T:C | C471R | 0.999 |
| 4:81046529:T:A | C370S | 0.998 |
| 4:81046529:T:C | C370R | 0.998 |
| 4:81046530:G:A | C370Y | 0.998 |
| 4:81046530:G:C | C370S | 0.998 |
dbSNP variants (sampled 300 via entrez): RS1000156707 (4:81043278 C>T), RS10002189 (4:81040543 A>C), RS1000572561 (4:81034006 T>A,C), RS10005851 (4:81050816 C>A,G), RS1000591139 (4:81040647 A>G), RS1000622284 (4:81040849 C>A,T), RS1000641037 (4:81032660 G>T), RS1000693240 (4:81039642 T>A), RS10007784 (4:81056536 C>A,G,T), RS1000800991 (4:81044363 T>A,C,G), RS1000814869 (4:81045252 A>G), RS1000901850 (4:81051488 CAG>C), RS1001314165 (4:81044143 T>C), RS1001507304 (4:81034282 A>G), RS1001657466 (4:81033737 A>G)
Disease associations
OMIM: gene MIM:112263 | disease phenotypes:
GenCC curated gene-disease
| Disease | Classification | Inheritance |
|---|---|---|
| coloboma | Moderate | Autosomal dominant |
Mondo (1): coloboma (MONDO:0001476)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
12 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000175_43 | Height | 2.000000e-06 |
| GCST001858_10 | Refractive error | 1.000000e-06 |
| GCST001876_7 | Pubertal anthropometrics | 1.000000e-07 |
| GCST003997_27 | Myopia | 2.000000e-23 |
| GCST006291_140 | Spherical equivalent or myopia (age of diagnosis) | 6.000000e-21 |
| GCST007159_3 | Corneal astigmatism | 1.000000e-06 |
| GCST007160_11 | Refractive astigmatism | 3.000000e-06 |
| GCST009462_55 | Optic disc size | 2.000000e-19 |
| GCST009959_24 | Retinal detachment or retinal break | 2.000000e-07 |
| GCST010002_9 | Refractive error | 2.000000e-65 |
| GCST012400_40 | Low myopia vs hyperopia | 1.000000e-09 |
| GCST90014268_14 | Cataracts | 3.000000e-12 |
EFO canonical traits (4, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0001382 | puberty |
| EFO:0004847 | age at onset |
| EFO:1002040 | Corneal astigmatism |
| EFO:0010698 | retinal break |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| D003103 | Coloboma | C11.250.110; C11.270.147; C16.131.384.282 |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
16 total (human), top 16 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | affects methylation, increases expression | 2 |
| ethyl-p-hydroxybenzoate | increases expression | 1 |
| monomethylarsonous acid | increases expression | 1 |
| bisphenol S | affects cotreatment, decreases methylation | 1 |
| Fulvestrant | affects cotreatment, decreases methylation | 1 |
| Air Pollutants | increases abundance, increases expression | 1 |
| Arsenic | increases methylation | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Lead | affects methylation | 1 |
| Rotenone | decreases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Valproic Acid | decreases methylation | 1 |
| Zearalenone | decreases expression | 1 |
| Aflatoxin B1 | decreases methylation | 1 |
| Okadaic Acid | decreases expression | 1 |
| Particulate Matter | increases expression, increases abundance | 1 |
Clinical trials (associated diseases)
4 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT00368004 | Not specified | TERMINATED | Family Studies of Uveal Coloboma |
| NCT01778543 | Not specified | RECRUITING | Pathogenesis and Genetics of Microphthalmia, Anophthalmia and Uveal Coloboma (MAC) |
| NCT04833361 | Not specified | COMPLETED | Potential Environmental Causes of Uveal Coloboma |
| NCT06293560 | Not specified | RECRUITING | Microphthalmia, Anophthalmia, and Coloboma Genetic Epidemiology in Children |
Related Atlas pages
- Associated diseases: coloboma
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cataract, coloboma, refractive error, retinal detachment