LMO3
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Also known as Rhom-3DAT1
Summary
LMO3 (LIM domain only 3, HGNC:6643) is a protein-coding gene on chromosome 12p12.3, encoding LIM domain only protein 3 (Q8TAP4).
The protein encoded by this gene belongs to the rhombotin family of cysteine-rich LIM domain oncogenes. This gene is predominantly expressed in the brain. Related family members, LMO1 and LMO2 on chromosome 11, have been reported to be involved in chromosomal translocations in T-cell leukemia. Many alternatively spliced transcript variants have been found for this gene.
Source: NCBI Gene 55885 — RefSeq curated summary.
At a glance
- GWAS associations: 9
- Clinical variants (ClinVar): 13 total
- MANE Select transcript:
NM_018640
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:6643 |
| Approved symbol | LMO3 |
| Name | LIM domain only 3 |
| Location | 12p12.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | Rhom-3, DAT1 |
| Ensembl gene | ENSG00000048540 |
| Ensembl biotype | protein_coding |
| OMIM | 180386 |
| Entrez | 55885 |
Gene structure
Transcript identifiers
Ensembl transcripts: 58 — 44 protein_coding, 8 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined, 2 retained_intron
ENST00000261169, ENST00000320122, ENST00000332914, ENST00000354662, ENST00000396205, ENST00000424192, ENST00000439600, ENST00000441439, ENST00000447609, ENST00000453727, ENST00000534946, ENST00000535535, ENST00000536172, ENST00000536509, ENST00000537304, ENST00000537568, ENST00000537757, ENST00000538020, ENST00000538051, ENST00000539232, ENST00000539534, ENST00000540445, ENST00000540590, ENST00000540848, ENST00000541295, ENST00000541589, ENST00000541764, ENST00000541846, ENST00000543721, ENST00000544276, ENST00000544754, ENST00000545436, ENST00000546279, ENST00000546281, ENST00000872904, ENST00000872905, ENST00000872906, ENST00000872907, ENST00000872908, ENST00000872909, ENST00000872910, ENST00000872911, ENST00000872912, ENST00000872913, ENST00000872914, ENST00000872915, ENST00000872916, ENST00000872917, ENST00000872918, ENST00000926579, ENST00000926580, ENST00000926581, ENST00000926582, ENST00000926583, ENST00000954699, ENST00000954700, ENST00000954701, ENST00000954702
RefSeq mRNA: 7 — MANE Select: NM_018640
NM_001001395, NM_001243609, NM_001243610, NM_001243611, NM_001243612, NM_001243613, NM_018640
CCDS: CCDS58210, CCDS58211, CCDS58212, CCDS8678
Canonical transcript exons
ENST00000537304 — 4 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001524225 | 16606066 | 16606162 |
| ENSE00002300197 | 16548372 | 16551327 |
| ENSE00003468813 | 16600655 | 16600868 |
| ENSE00003786546 | 16560413 | 16560538 |
Expression profiles
Bgee: expression breadth ubiquitous, 249 present calls, max score 99.58.
FANTOM5 (CAGE): breadth broad, TPM avg 12.8004 / max 1133.9355, expressed in 536 samples.
FANTOM5 promoters (32 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 129970 | 4.8371 | 392 |
| 129958 | 1.4134 | 268 |
| 129981 | 1.2140 | 162 |
| 129971 | 0.8065 | 204 |
| 129972 | 0.6432 | 120 |
| 129977 | 0.5447 | 207 |
| 129966 | 0.4435 | 170 |
| 129959 | 0.3089 | 132 |
| 129984 | 0.2880 | 55 |
| 129960 | 0.2556 | 135 |
Top tissues by expression
297 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| middle temporal gyrus | UBERON:0002771 | 99.58 | gold quality |
| Brodmann (1909) area 46 | UBERON:0006483 | 99.30 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 99.19 | gold quality |
| orbitofrontal cortex | UBERON:0004167 | 99.18 | gold quality |
| superior frontal gyrus | UBERON:0002661 | 99.11 | gold quality |
| entorhinal cortex | UBERON:0002728 | 99.05 | gold quality |
| endothelial cell | CL:0000115 | 99.04 | gold quality |
| cortical plate | UBERON:0005343 | 99.02 | gold quality |
| postcentral gyrus | UBERON:0002581 | 98.77 | gold quality |
| parietal lobe | UBERON:0001872 | 98.55 | gold quality |
| cranial nerve II | UBERON:0000941 | 98.54 | gold quality |
| temporal lobe | UBERON:0001871 | 98.04 | gold quality |
| nucleus accumbens | UBERON:0001882 | 97.97 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 97.97 | gold quality |
| CA1 field of hippocampus | UBERON:0003881 | 97.97 | gold quality |
| caudate nucleus | UBERON:0001873 | 97.86 | gold quality |
| calcaneal tendon | UBERON:0003701 | 97.84 | gold quality |
| prefrontal cortex | UBERON:0000451 | 97.83 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 97.73 | gold quality |
| primary visual cortex | UBERON:0002436 | 97.60 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 97.57 | gold quality |
| amygdala | UBERON:0001876 | 97.54 | gold quality |
| putamen | UBERON:0001874 | 97.51 | gold quality |
| frontal cortex | UBERON:0001870 | 97.42 | gold quality |
| frontal lobe | UBERON:0016525 | 97.42 | gold quality |
| telencephalon | UBERON:0001893 | 97.39 | gold quality |
| cerebral cortex | UBERON:0000956 | 97.38 | gold quality |
| neocortex | UBERON:0001950 | 97.25 | gold quality |
| occipital lobe | UBERON:0002021 | 97.16 | gold quality |
| cingulate cortex | UBERON:0003027 | 96.51 | gold quality |
Single-cell (SCXA)
Detected in 9 experiment(s), a significant marker in 9.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-HCAD-5 | yes | 1153.94 |
| E-MTAB-9154 | yes | 677.85 |
| E-MTAB-8894 | yes | 580.28 |
| E-MTAB-8530 | yes | 214.00 |
| E-GEOD-98556 | yes | 183.29 |
| E-ANND-3 | yes | 22.44 |
| E-HCAD-1 | yes | 20.64 |
| E-GEOD-130148 | yes | 10.09 |
| E-ENAD-27 | yes | 4.10 |
Regulation
Is transcription factor: yes
Downstream targets (CollecTRI)
2 targets.
| Target | Regulation |
|---|---|
| ASCL1 | Activation |
| HES1 | Repression |
Upstream regulators (CollecTRI, top): ARX, EBF3, EGR1, ETS2, GBX2, LHX2, LHX9, NKX2-1, NR3C1, TP53
miRNA regulators (miRDB)
137 targeting LMO3, 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-3924 | 100.00 | 72.09 | 2394 |
| 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-4262 | 100.00 | 73.26 | 3931 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-5692A | 100.00 | 74.40 | 6850 |
| HSA-MIR-6867-5P | 100.00 | 82.21 | 3464 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-3662 | 99.99 | 73.82 | 5684 |
| HSA-MIR-548P | 99.98 | 72.25 | 3784 |
| HSA-MIR-4775 | 99.98 | 75.00 | 6394 |
| HSA-LET-7F-2-3P | 99.98 | 70.98 | 2588 |
| HSA-MIR-1185-1-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-1185-2-3P | 99.98 | 71.04 | 2593 |
| HSA-MIR-520D-5P | 99.98 | 73.34 | 4883 |
| HSA-MIR-524-5P | 99.98 | 73.43 | 4882 |
| HSA-MIR-3148 | 99.97 | 75.06 | 6478 |
| HSA-MIR-548AT-5P | 99.96 | 70.83 | 2666 |
| HSA-MIR-590-3P | 99.96 | 74.34 | 6478 |
| HSA-MIR-4666A-3P | 99.96 | 71.71 | 3434 |
| HSA-MIR-302E | 99.96 | 70.74 | 2669 |
| HSA-MIR-9-3P | 99.96 | 70.88 | 2068 |
| HSA-MIR-141-3P | 99.94 | 72.79 | 2421 |
| HSA-MIR-200A-3P | 99.94 | 72.68 | 2420 |
| HSA-MIR-381-3P | 99.93 | 71.87 | 2854 |
| HSA-MIR-218-5P | 99.93 | 72.22 | 2103 |
| HSA-MIR-300 | 99.92 | 71.76 | 2856 |
| HSA-MIR-10527-5P | 99.91 | 72.28 | 3754 |
Literature-anchored findings (GeneRIF, showing 18)
- The deregulated expression of neuronal-specific LMO3 and HEN2 contributes to the genesis and progression of human neuroblastoma in a lineage-specific manner. (PMID:15930276)
- LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation without inhibition of its DNA-binding activity. (PMID:19995558)
- The present results suggest that a transcriptional complex of LMO3 and HEN2 may contribute to the genesis and malignant phenotype of neuroblastoma by inhibiting HES1 which suppresses the transactivation of Mash1. (PMID:21573214)
- We confirmed that the expression of LMO3 in squamous cell carcinoma is regulated by DNA methylation of its specific promoter region. (PMID:22011669)
- suggest that LMO3 is a transcriptional signal transducer in NKX2-1-amplified lung adenocarcinomas (PMID:23322301)
- LMO3 as a regulator of human adipogenesis and could contribute a mechanism resulting in visceral-fat accumulation in obesity due to excess glucocorticoids. (PMID:23823477)
- MiR-101 decreased the expression of LMO3 by reversing the methylation status of the LMO3 promoter and by inhibiting the presence of the methylation-related histones H3K4me2 and H3K27me3 and increasing the presence of H3K9me3 and H4K20me3 on the promoter. (PMID:25829251)
- SH3BP5, LMO3, and SNAP25 were expressed in diffuse large B-cell lymphoma cells and associated with clinical features. (PMID:27184832)
- LMO3 attenuates GATA4-dependent, BMP2-mediated inflammatory endothelial activation. (PMID:28669928)
- These results suggested that LMO3 promotes Gastric Cancer cell invasion and proliferation mainly through Akt/mTOR and Akt/GSK3beta signaling. (PMID:29436606)
- These results suggest that LMO3 promotes hepatocellular carcinoma (HCC) cell invasion and anoikis inhibition by interacting with LATS1 and suppressing Hippo signaling. LMO3 may serve as a potential therapeutic target for HCC in future (PMID:30219064)
- our results suggest that LMO3-BORCS5 fusion oncogene plays an essential role in tumorigenesis (PMID:31488873)
- MicroRNA-381 inhibits lung adenocarcinoma cell biological progression by directly targeting LMO3 through regulation of the PI3K/Akt signaling pathway and epithelial-to-mesenchymal transition. (PMID:31646571)
- LMO3 reprograms visceral adipocyte metabolism during obesity. (PMID:34018016)
- Transcriptomic analysis and biological evaluation reveals that LMO3 regulates the osteogenic differentiation of human adipose derived stem cells via PI3K/Akt signaling pathway. (PMID:35165791)
- Hyperglycemia affects neuronal differentiation and Nestin, FOXO1, and LMO3 mRNA expression of human Wharton’s jelly mesenchymal stem cells of children from diabetic mothers. (PMID:36413852)
- Circ_0007385 promotes the proliferation and inhibits the apoptosis of non-small cell lung cancer cells via miR-337-3p-dependent regulation of LMO3. (PMID:36426731)
- LMO3 is a suppressor of the basal-like/squamous subtype and reduces disease aggressiveness of pancreatic cancer through glycerol 3-phosphate metabolism. (PMID:38366633)
Cross-species orthologs
3 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | lmo3 | ENSDARG00000008720 |
| mus_musculus | Lmo3 | ENSMUSG00000030226 |
| rattus_norvegicus | Lmo3 | ENSRNOG00000047450 |
Paralogs (20): FHL1 (ENSG00000022267), LHX5 (ENSG00000089116), ZFHX4 (ENSG00000091656), LHX2 (ENSG00000106689), LHX6 (ENSG00000106852), LHX3 (ENSG00000107187), LHX4 (ENSG00000121454), LMO2 (ENSG00000135363), ZFHX2 (ENSG00000136367), LMX1B (ENSG00000136944), ZFHX3 (ENSG00000140836), LMO4 (ENSG00000143013), LHX9 (ENSG00000143355), CRIP3 (ENSG00000146215), LHX8 (ENSG00000162624), LMX1A (ENSG00000162761), LMO1 (ENSG00000166407), CRIP2 (ENSG00000182809), CRIP1 (ENSG00000213145), LHX1 (ENSG00000273706)
Protein
Protein identifiers
LIM domain only protein 3 — Q8TAP4 (reviewed: Q8TAP4)
Alternative names: Neuronal-specific transcription factor DAT1, Rhombotin-3
All UniProt accessions (11): C9JE61, Q8TAP4, F5GYZ6, F5GZR3, F5H2N9, F5H3S4, F5H4K9, F5H4T0, F5H655, F6TDU8, Q05D86
Isoforms (4)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8TAP4-1 | 1 | yes |
| Q8TAP4-2 | 2 | |
| Q8TAP4-3 | 3 | |
| Q8TAP4-4 | 4 |
RefSeq proteins (7): NP_001001395, NP_001230538, NP_001230539, NP_001230540, NP_001230541, NP_001230542, NP_061110* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR001781 | Znf_LIM | Domain |
| IPR050945 | LMO_RBTN_TF | Family |
Pfam: PF00412
UniProt features (7 total): splice variant 3, domain 2, chain 1, sequence conflict 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8TAP4-F1 | 88.38 | 0.79 |
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 301 (showing top):
GOBP_NEGATIVE_REGULATION_OF_ERK1_AND_ERK2_CASCADE, YAATNRNNNYNATT_UNKNOWN, GOBP_REGULATION_OF_FAT_CELL_DIFFERENTIATION, FREAC2_01, RORA1_01, GOBP_CELLULAR_RESPONSE_TO_LIPID, NKX25_02, GCANCTGNY_MYOD_Q6, CMYB_01, GOBP_POSITIVE_REGULATION_OF_FAT_CELL_DIFFERENTIATION, AREB6_03, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY, GOBP_REGULATION_OF_INTRACELLULAR_STEROID_HORMONE_RECEPTOR_SIGNALING_PATHWAY, TGACCTY_ERR1_Q2, TACAATC_MIR508
GO Biological Process (5): positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360), positive regulation of fat cell differentiation (GO:0045600), positive regulation of transcription by RNA polymerase II (GO:0045944), negative regulation of ERK1 and ERK2 cascade (GO:0070373), positive regulation of nuclear receptor-mediated glucocorticoid signaling pathway (GO:2000324)
GO Molecular Function (4): transcription coactivator activity (GO:0003713), metal ion binding (GO:0046872), DNA-binding transcription factor binding (GO:0140297), protein binding (GO:0005515)
GO Cellular Component (2): nucleus (GO:0005634), cytoplasm (GO:0005737)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| positive regulation of DNA-templated transcription | 2 |
| peroxisome proliferator activated receptor signaling pathway | 1 |
| regulation of peroxisome proliferator activated receptor signaling pathway | 1 |
| positive regulation of intracellular signal transduction | 1 |
| fat cell differentiation | 1 |
| positive regulation of cell differentiation | 1 |
| regulation of fat cell differentiation | 1 |
| regulation of transcription by RNA polymerase II | 1 |
| transcription by RNA polymerase II | 1 |
| negative regulation of MAPK cascade | 1 |
| ERK1 and ERK2 cascade | 1 |
| regulation of ERK1 and ERK2 cascade | 1 |
| positive regulation of intracellular steroid hormone receptor signaling pathway | 1 |
| nuclear receptor-mediated glucocorticoid signaling pathway | 1 |
| regulation of nuclear receptor-mediated glucocorticoid signaling pathway | 1 |
| transcription coregulator activity | 1 |
| cation binding | 1 |
| transcription factor binding | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular anatomical structure | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
0 interactions, top by confidence (×1000):
IntAct
71 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| LMO3 | FBLIM1 | psi-mi:“MI:0915”(physical association) | 0.670 |
| LDB1 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.670 |
| LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| SP4 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | IKZF1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| FOS | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| KCTD1 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | TAX1BP1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NUTM1 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CEP57L1 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| SAMD3 | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| BANP | LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | CBY2 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | FAM131C | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| LMO3 | NUTM1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LMO3 | SAMD3 | psi-mi:“MI:0915”(physical association) | 0.560 |
BioGRID (164): LMO3 (Two-hybrid), LMO3 (Two-hybrid), LMO3 (Two-hybrid), LMO3 (Two-hybrid), LMO3 (Two-hybrid), LMO3 (Two-hybrid), LMO3 (Two-hybrid), CCDC33 (Two-hybrid), SAMD3 (Two-hybrid), SPERT (Two-hybrid), NUTM1 (Two-hybrid), KCTD1 (Two-hybrid), NBPF22P (Two-hybrid), CEP57L1 (Two-hybrid), FAM131C (Two-hybrid)
ESM2 similar proteins: A0A324, A1XQR9, A4FUI2, A5JSS2, A6MZM2, G1SHQ2, O09167, O14602, O35900, O60739, P20280, P25800, P41567, P46778, P47813, P48024, P49666, P51971, P61220, P62303, P62304, P62305, P62308, P62309, Q09028, Q0D5W6, Q0P5B3, Q2KIA3, Q3B8H4, Q3ZBL0, Q4R4X9, Q503U0, Q5E938, Q5RA42, Q5RBW7, Q5RFF4, Q60872, Q60972, Q6GVM3, Q6QN05
Diamond homologs: A0JNI8, A2I8Z7, A2PZF9, G5EC36, G5EE86, O14639, O35652, O60663, O88609, O94929, O97581, P20154, P25791, P25800, P25801, P29673, P29674, P34764, P34765, P36198, P36200, P37137, P48742, P50211, P50212, P50458, P50480, P50481, P52889, P53405, P53406, P53407, P53408, P53409, P53410, P53411, P53412, P53413, P53667, P53668
SIGNOR signaling
3 interactions.
| A | Effect | B | Mechanism |
|---|---|---|---|
| LMO3 | “up-regulates quantity by expression” | ASCL1 | “transcriptional regulation” |
| LMO3 | “down-regulates quantity by repression” | HES1 | “transcriptional regulation” |
| LMO3 | “up-regulates activity” | NHLH2 | binding |
Disease & clinical
Clinical variants and AI predictions
ClinVar
13 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 9 |
| Likely benign | 1 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1319 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 12:16560408:CTTA:C | donor_loss | 1.0000 |
| 12:16560409:TTAC:T | donor_loss | 1.0000 |
| 12:16560410:TA:T | donor_loss | 1.0000 |
| 12:16560411:A:C | donor_loss | 1.0000 |
| 12:16560412:CCT:C | donor_gain | 1.0000 |
| 12:16560535:GAGCC:G | acceptor_loss | 1.0000 |
| 12:16560537:GC:G | acceptor_gain | 1.0000 |
| 12:16560537:GCCTA:G | acceptor_loss | 1.0000 |
| 12:16560538:CC:C | acceptor_gain | 1.0000 |
| 12:16560538:CCT:C | acceptor_loss | 1.0000 |
| 12:16560539:C:CA | acceptor_loss | 1.0000 |
| 12:16560539:C:CC | acceptor_gain | 1.0000 |
| 12:16560540:T:A | acceptor_loss | 1.0000 |
| 12:16590509:A:AC | donor_gain | 1.0000 |
| 12:16600746:T:TA | donor_gain | 1.0000 |
| 12:16600864:TATAC:T | acceptor_gain | 1.0000 |
| 12:16600865:ATAC:A | acceptor_gain | 1.0000 |
| 12:16600866:TAC:T | acceptor_gain | 1.0000 |
| 12:16600866:TACC:T | acceptor_loss | 1.0000 |
| 12:16600869:C:CC | acceptor_gain | 1.0000 |
| 12:16600869:CTAAA:C | acceptor_loss | 1.0000 |
| 12:16560411:A:AC | donor_gain | 0.9900 |
| 12:16560412:C:CC | donor_gain | 0.9900 |
| 12:16560535:GAGC:G | acceptor_gain | 0.9900 |
| 12:16600688:G:C | donor_gain | 0.9900 |
| 12:16600729:G:C | donor_gain | 0.9900 |
| 12:16600867:AC:A | acceptor_gain | 0.9900 |
| 12:16600868:CC:C | acceptor_gain | 0.9900 |
| 12:16560534:AGAGC:A | acceptor_gain | 0.9800 |
| 12:16600727:CAG:C | donor_gain | 0.9800 |
AlphaMissense
0 scored. Top likely-pathogenic:
dbSNP variants (sampled 300 via entrez): RS1000057979 (12:16571474 A>C,G), RS1000114524 (12:16597654 T>G), RS1000149954 (12:16553826 G>C), RS1000166838 (12:16598084 T>C), RS1000198643 (12:16597521 G>A), RS1000321476 (12:16590844 C>A,T), RS1000357048 (12:16584294 T>C), RS1000363048 (12:16577517 T>C), RS1000451951 (12:16583831 T>C), RS1000497894 (12:16610675 A>C), RS1000579223 (12:16578368 T>C), RS1000606781 (12:16554270 T>C), RS1000668593 (12:16597222 A>G,T), RS1000738511 (12:16571847 T>C), RS1000742910 (12:16560095 A>G,T)
Disease associations
OMIM: gene MIM:180386 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
9 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST006946_11 | Worry too long after an embarrassing experience | 8.000000e-10 |
| GCST007277_16 | Tourette syndrome | 1.000000e-06 |
| GCST007576_138 | Chronotype | 2.000000e-10 |
| GCST009524_200 | Household income (MTAG) | 6.000000e-09 |
| GCST011461_2 | Barrett’s esophagus or Esophageal adenocarcinoma | 1.000000e-08 |
| GCST011461_7 | Barrett’s esophagus or Esophageal adenocarcinoma | 5.000000e-09 |
| GCST011462_2 | Barrett’s esophagus or esophageal adenocarcinoma x sex interaction (2df test) | 4.000000e-08 |
| GCST011584_1 | Metastatic colorectal cancer survival in treatment with chemotherapy plus biologics | 1.000000e-06 |
| GCST011703_7 | Smoking initiation | 2.000000e-08 |
EFO canonical traits (7, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0009589 | worry measurement |
| EFO:0008328 | chronotype measurement |
| EFO:0009695 | household income |
| EFO:0008343 | sex interaction measurement |
| EFO:0000714 | survival time |
| EFO:1001480 | metastatic colorectal cancer |
| EFO:0005670 | smoking initiation |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
43 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects expression, increases methylation, affects cotreatment, decreases expression | 8 |
| methylmercuric chloride | decreases expression | 3 |
| trichostatin A | affects cotreatment, decreases expression | 3 |
| Dexamethasone | affects cotreatment, increases expression | 3 |
| Estradiol | decreases expression | 3 |
| Ethinyl Estradiol | affects expression, decreases expression | 3 |
| mercuric bromide | decreases expression, affects cotreatment | 2 |
| entinostat | decreases expression, affects cotreatment | 2 |
| belinostat | decreases expression, affects cotreatment | 2 |
| Panobinostat | affects cotreatment, decreases expression | 2 |
| Nickel | decreases expression | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| 1-Methyl-3-isobutylxanthine | affects cotreatment, increases expression | 2 |
| Genistein | decreases expression | 2 |
| p-Chloromercuribenzoic Acid | affects cotreatment, decreases expression | 2 |
| bisphenol A | affects expression | 1 |
| arsenite | increases methylation | 1 |
| sodium arsenite | decreases expression | 1 |
| tetrabromobisphenol A | increases expression | 1 |
| tobacco tar | decreases expression, decreases reaction | 1 |
| allyl sulfide | decreases expression, decreases reaction | 1 |
| beta-methylcholine | affects expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| dorsomorphin | decreases expression, affects cotreatment | 1 |
| Temozolomide | increases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Benzo(a)pyrene | decreases methylation, affects methylation | 1 |
| Dichlorodiphenyl Dichloroethylene | increases expression | 1 |
| Diethylhexyl Phthalate | decreases expression | 1 |
| Indomethacin | increases expression, affects cotreatment | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): Barrett esophagus, esophageal adenocarcinoma