LMO2

Summary

LMO2 (LIM domain only 2, HGNC:6642) is a protein-coding gene on chromosome 11p13, encoding Rhombotin-2 (P25791). Acts with TAL1/SCL to regulate red blood cell development.

LMO2 encodes a cysteine-rich, two LIM-domain protein that is required for yolk sac erythropoiesis. The LMO2 protein has a central and crucial role in hematopoietic development and is highly conserved. The LMO2 transcription start site is located approximately 25 kb downstream from the 11p13 T-cell translocation cluster (11p13 ttc), where a number T-cell acute lymphoblastic leukemia-specific translocations occur. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 4005 — RefSeq curated summary.

At a glance

• GWAS associations: 13
• Clinical variants (ClinVar): 43 total
• Druggable target: yes
• Transcription factor: yes — 33 downstream targets (CollecTRI)
• MANE Select transcript: NM_005574

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:6642
Approved symbol	LMO2
Name	LIM domain only 2
Location	11p13
Locus type	gene with protein product
Status	Approved
Aliases	TTG2, RHOM2, RBTN2
Ensembl gene	ENSG00000135363
Ensembl biotype	protein_coding
OMIM	180385
Entrez	4005

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000257818, ENST00000395833, ENST00000411482, ENST00000464025, ENST00000465614, ENST00000493667, ENST00000969327

RefSeq mRNA: 3 — MANE Select: NM_005574 NM_001142315, NM_001142316, NM_005574

CCDS: CCDS44567, CCDS7888

Canonical transcript exons

ENST00000257818 — 6 exons

Exon	Start	End
ENSE00001004239	33864602	33864817
ENSE00001308883	33881824	33881887
ENSE00001316816	33869710	33869987
ENSE00001329752	33891795	33892076
ENSE00001632415	33869346	33869586
ENSE00003620619	33858576	33859575

Expression profiles

Bgee: expression breadth ubiquitous, 293 present calls, max score 98.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 9.6103 / max 206.8389, expressed in 979 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
119224	4.4870	820
119229	1.6807	392
119225	1.5091	567
119235	0.9414	180
119234	0.7046	77
119226	0.2230	98
119227	0.0315	9
119236	0.0204	4
119228	0.0125	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
monocyte	CL:0000576	98.21	gold quality
tendon of biceps brachii	UBERON:0008188	98.19	gold quality
mononuclear cell	CL:0000842	98.08	gold quality
leukocyte	CL:0000738	97.90	gold quality
trabecular bone tissue	UBERON:0002483	97.73	gold quality
urethra	UBERON:0000057	96.92	gold quality
endothelial cell	CL:0000115	95.88	gold quality
vena cava	UBERON:0004087	95.33	gold quality
inferior vagus X ganglion	UBERON:0005363	95.31	gold quality
gluteal muscle	UBERON:0002000	94.90	gold quality
medial globus pallidus	UBERON:0002477	94.89	gold quality
layer of synovial tissue	UBERON:0007616	94.83	gold quality
synovial joint	UBERON:0002217	94.75	gold quality
renal medulla	UBERON:0000362	94.74	gold quality
type B pancreatic cell	CL:0000169	94.69	gold quality
subthalamic nucleus	UBERON:0001906	94.65	gold quality
bone marrow	UBERON:0002371	94.64	gold quality
superior vestibular nucleus	UBERON:0007227	94.60	gold quality
medulla oblongata	UBERON:0001896	94.44	gold quality
globus pallidus	UBERON:0001875	94.38	gold quality
granulocyte	CL:0000094	94.37	gold quality
epithelium of bronchus	UBERON:0002031	94.12	gold quality
bronchus	UBERON:0002185	94.11	gold quality
lower lobe of lung	UBERON:0008949	94.03	gold quality
bronchial epithelial cell	CL:0002328	93.89	gold quality
lateral globus pallidus	UBERON:0002476	93.77	gold quality
penis	UBERON:0000989	93.75	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	93.57	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	93.51	gold quality
vastus lateralis	UBERON:0001379	93.42	gold quality

Single-cell (SCXA)

Detected in 10 experiment(s), a significant marker in 9.

Experiment	Marker?	Max mean expression
E-GEOD-135922	yes	1445.89
E-MTAB-9388	yes	76.09
E-HCAD-6	yes	41.93
E-MTAB-6701	yes	26.94
E-MTAB-8271	yes	15.37
E-ANND-3	yes	12.57
E-MTAB-8498	yes	10.23
E-CURD-112	yes	8.55
E-MTAB-10553	yes	6.72
E-MTAB-6386	no	374.05

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

33 targets.

Target	Regulation
ANGPT2	Unknown
BEX2
CA1
CD4	Activation
CDH1	Repression
CDH17
CDH5
ELK1	Unknown
ERG	Activation
FGF2	Activation
FLI1
GYPA	Repression
HBB
HBG1
HHEX
JAK2
LCK
LDB1
LEF1	Repression
LMO1
LMO2
LYL1	Unknown
MECOM
MT1A
NFATC1	Activation
NFE2
NRP2	Unknown
PLEK
PRDM16
SPTA1

Upstream regulators (CollecTRI, top): CTNNB1, ELF1, ERG, ETS1, ETV2, FLI1, HLF, LMO2, MYB, MYCN, PRDM1, SPI1, TAL1, TCF3, TEF

miRNA regulators (miRDB)

41 targeting LMO2, 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-3163	100.00	77.23	8605
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-8062	99.88	68.43	995
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-659-3P	99.85	70.69	1620
HSA-MIR-4698	99.84	71.41	4303
HSA-MIR-4659A-3P	99.80	72.62	4248
HSA-MIR-4659B-3P	99.80	72.62	4248
HSA-MIR-623	99.76	68.16	1170
HSA-MIR-7157-5P	99.66	69.33	1829
HSA-MIR-5003-5P	99.61	69.13	1624
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-3182	99.40	68.15	2454
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-935	98.82	69.36	1072
HSA-MIR-210-5P	98.57	64.37	832
HSA-MIR-6773-3P	98.17	65.51	1213
HSA-MIR-4469	97.93	65.81	1319

Literature-anchored findings (GeneRIF, showing 40)

• Negative regulatory elements are present in the human LMO2 oncogene and may contribute to its expression in leukemia. (PMID:15541480)
• Therapies directed against LMO2 may be important for treatment of hemangioma because of hemangioma’s limited localization and the fact that LMO2-associated protein complexes could regulate angiogenesis. (PMID:16793212)
• identification of a new recurrent and cryptic deletion on chromosome 11 (del(11)(p12p13)) in about 4% (6/138) of pediatric T-ALL patients that activates the LMO2 oncogene in 4 of 6 del(11)(p12p13)-positive T-ALL patients (PMID:16873670)
• LMO2 protein is expressed in normal germinal-center (GC) B cells and GC-derived B-cell lines and in a subset of GC-derived B-cell lymphomas, also in erythroid and myeloid precursors, megakaryocytes, and in lymphoblastic and acute myeloid leukemias. (PMID:17038524)
• LMO2 is most highly transcribed in CD34+ progenitor cells. Upon stimulation with growth factors typically used in gene therapy protocols transcription of LMO2. (PMID:17268520)
• critical role for the exact breakpoint location in determining LMO2 activation levels and the consequent pressure for T-ALL development. (PMID:17360939)
• the SCL-LMO2 interaction couples protein stabilization with higher order protein complex assembly, thus providing a powerful means of modulating the stoichiometry and spatiotemporal activity of SCL complexes (PMID:17878155)
• characterize the assembly of a five-component complex containing TAL1, LMO2, Ldb1, E12, and DNA. The bHLH domains of TAL1 and E12 alone primarily formed helical homodimers, but together formed heterodimers, to which LMO2 bound with high affinity (PMID:17910069)
• Both LMO2 and LMO4 interacted strongly to LDB1, which was required for their localization to the nucleus. (PMID:17964543)
• LMO2 associated with the endogenous human miR-142 promoter; LMO2 appeared to play a pivotal function in negatively regulating the expression of miR-142. (PMID:17972953)
• biallelic activation of LMO2 in immature T-ALL cases may reflect their early T-cell development stage rather than it represents a true oncogenic mechanism. (PMID:18079736)
• LMO2, TAL1, Ttg-1, and SIL support levels of V(D)J recombination above background levels in cell culture and are also cleaved by the RAG proteins, while Hox11 and SCL are nicked but not cleaved efficiently in vitro (PMID:18187418)
• LMO2-C can bind endogenous GATA1 and LDB1 protein in K562 cells and downregulate the expression of hematopoietic specific gene glycoprotein. (PMID:18844071)
• GC-enriched hsa-miR-125b down-regulates the expression of IRF4 and PRDM1/BLIMP1, and memory B cell-enriched hsa-miR-223 down-regulates the expression of LMO2. (PMID:19047678)
• The restricted expression pattern, nuclear localization, and crisp staining of LMO2 in paraffin blocks make it an attractive candidate for the diagnostic immunohistochemistry laboratory. (PMID:19141387)
• decline of miR-223 is an important event for erythroid differentiation that leads to the expansion of erythroblast cells at least partially mediated by unblocking LMO2 protein expression (PMID:19278969)
• LMO2 is regulated at both a posttranscriptional and post-translational level in erythroid progenitors during erythropoiesis.[review] (PMID:19336746)
• Lmo2 is, therefore, required for sustained T-cell tumor growth, in addition to its preleukemic effect. (PMID:19487290)
• LMO2 is a promising marker for predicting a better prognosis in pancreatic cancer. (PMID:19568416)
• LMO2 protein expression is correlated with improved hematologic remission and overall survival in the CML patients treated with IM. (PMID:19635185)
• The abnormal expression and protein interaction of LMO2 and LYL1 may play a role in the abnormal proliferation and differentiation of myeloid hematopoietic cells. (PMID:19671288)
• Homo-binding character of LMO2 isoforms and their synergic and antagonistic functions regulate hematopoietic-related target genes. (PMID:20346173)
• E2A-HLF promotes cell survival of t(17;19)- acute lymphoblastic leukemia cells by aberrantly up-regulating LMO2 expression (PMID:20519628)
• We report that LMO2 protein is expressed in a significant proportion of B-ALL and AML and the staining of LMO2 protein does not predict survival in acute leukemia. (PMID:20557670)
• The findings suggest LMO2 as a potential marker for the germinal center B-cell phenotype of diffuse large B-cell lymphoma. (PMID:20660332)
• a self-sustaining triad of LMO2/ERG/FLI1 stabilizes the expression of important mediators of the leukaemic phenotype such as HHEX/PRH. (PMID:20676125)
• Overexpression of either KLF1 or LMO2 partially rescued the defect in erythropoiesis caused by c-myb silencing, whereas only KLF1 was also able to repress the megakaryocyte differentiation enhanced in Myb-silenced CD34+ cells. (PMID:20686118)
• Our results show that HGAL and LMO2 are sensitive markers for follicular lymphoma diagnosis. (PMID:20697248)
• ectopically expressed LMO2 impaired the function of DeltaEF1 in both transcriptional and protein levels and identified DeltaEF1 as a novel pathogenic target of LMO2 in T-cell leukemia. (PMID:20731704)
• LMO2 probably promotes angiogenesis by up-regulation of bFGF expression and thereby consequently influences progression of infantile haemangiomas (PMID:20955387)
• Multiple-wavelength anomalous dispersion (MAD) data have been collected at the zinc X-ray absorption edge to a resolution of 2.8 A and the data were used to solve the structure of the LMO2:Ldb1-LIM-interaction domain complex. (PMID:21045296)
• As LMO2 controls hematopoiesis, its dysregulation is leukemogenic (PMID:21059912)
• both Lmo2 and Bcl-2 are required for the action of E2A-HLF in leukemogenesis (PMID:21072044)
• first structural model of the DNA-binding complex containing LMO2, LDB1, SCL/TAL1, and GATA-1 (PMID:21076045)
• SStudies suggest that the expression of LMO2 protein in lymphoma tissue biopsies predicts survival in patients with RA who have developed DLBCL (PMID:21375434)
• B-cell acute lymphoblastic leukemia cases expressed variable levels of LMO2 depending on immunophenotypical and cytogenetic features (PMID:21459790)
• LMO2 is sensitive and specific marker for detecting follicular lymphoma in nodal and extranodal sites (PMID:21502424)
• The measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with diffuse large B-cell lymphoma. (PMID:21670469)
• Data suggest that both HGAL and LMO2 are directly regulated by the transcription repressor PRDM1–overexpression of PRDM1 down-regulates HGAL and LMO2; PRDM1 directly binds to promoters of both HGAL and LMO2 and represses genetic transcription. (PMID:21722313)
• Germline genetic variation in LMO2 was associated with diffuse large B-cell lymphoma prognosis and provided slightly stronger predictive ability relative to LMO2 immunohistochemistry status. (PMID:22066713)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	lmo2	ENSDARG00000095019
mus_musculus	Lmo2	ENSMUSG00000032698
rattus_norvegicus	Lmo2	ENSRNOG00000009401

Paralogs (20): FHL1 (ENSG00000022267), LMO3 (ENSG00000048540), LHX5 (ENSG00000089116), ZFHX4 (ENSG00000091656), LHX2 (ENSG00000106689), LHX6 (ENSG00000106852), LHX3 (ENSG00000107187), LHX4 (ENSG00000121454), 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

Rhombotin-2 — P25791 (reviewed: P25791)

Alternative names: Cysteine-rich protein TTG-2, LIM domain only protein 2, T-cell translocation protein 2

All UniProt accessions (1): P25791

UniProt curated annotations — full annotation on UniProt →

Function. Acts with TAL1/SCL to regulate red blood cell development. Also acts with LDB1 to maintain erythroid precursors in an immature state.

Subunit / interactions. Interacts via its LIM domains with ELF2 and LDB1. Also interacts with basic helix-loop-helix protein TAL1/SCL and can assemble in a complex with LMO2 and TAL1/SCL. Interacts with BEX2 and KDM5A.

Subcellular location. Nucleus.

Disease relevance. A chromosomal aberration involving LMO2 may be a cause of a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(11,14)(p13;q11) with TCRD.

Domain organisation. The second LIM zinc-binding domain interacts with KDM5A.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Isoforms (3)

UniProt ID	Names	Canonical?
P25791-1	1, LMO2a	yes
P25791-3	3
P25791-4	2

RefSeq proteins (3): NP_001135787, NP_001135788, NP_005565* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001781	Znf_LIM	Domain
IPR050945	LMO_RBTN_TF	Family

Pfam: PF00412

UniProt features (25 total): strand 8, turn 7, helix 4, splice variant 3, domain 2, chain 1

Structure

Experimental structures (PDB)

4 structures.

PDB	Method	Resolution (Å)
2XJY	X-RAY DIFFRACTION	2.4
2XJZ	X-RAY DIFFRACTION	2.8
2YPA	X-RAY DIFFRACTION	2.8
4KFZ	X-RAY DIFFRACTION	2.8

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P25791-F1	90.73	0.77

Antibody-complex structures (SAbDab): 1 — 4KFZ

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-8939236	RUNX1 regulates transcription of genes involved in differentiation of HSCs

MSigDB gene sets: 382 (showing top): MODULE_52, GOBP_EMBRYONIC_HEMOPOIESIS, MODULE_169, PEREZ_TP63_TARGETS, MODULE_45, MODULE_128, RIZKI_TUMOR_INVASIVENESS_3D_DN, MODULE_16, ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN, EVI1_05, MODULE_66, MODULE_118, GROSS_HYPOXIA_VIA_ELK3_ONLY_DN

GO Biological Process (1): positive regulation of transcription by RNA polymerase II (GO:0045944)

GO Molecular Function (8): transcription coregulator binding (GO:0001221), transcription coactivator activity (GO:0003713), identical protein binding (GO:0042802), bHLH transcription factor binding (GO:0043425), metal ion binding (GO:0046872), RNA polymerase II-specific DNA-binding transcription factor binding (GO:0061629), DNA-binding transcription factor binding (GO:0140297), protein binding (GO:0005515)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Transcriptional regulation by RUNX1	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
positive regulation of DNA-templated transcription	2
transcription factor binding	2
DNA-binding transcription factor binding	2
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
transcription coregulator activity	1
protein binding	1
cation binding	1
binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
protein-containing complex	1

Protein interactions and networks

STRING

1864 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LMO2	TAL1	P17542	999
LMO2	LDB1	Q86U70	999
LMO2	LDB2	O43679	998
LMO2	LYL1	P12980	997
LMO2	GATA1	P15976	996
LMO2	GATA2	P23769	994
LMO2	TCF3	P15883	993
LMO2	RUNX1	Q01196	977
LMO2	ZFPM1	Q8IX07	972
LMO2	BEX2	Q9BXY8	896
LMO2	BEX1	Q9HBH7	895
LMO2	CCND2	P30279	848
LMO2	BCL6	P41182	842
LMO2	GFI1B	Q5VTD9	839
LMO2	AFDN	P55196	820

IntAct

246 interactions, top by confidence:

A	B	Type	Score
LMO2	MAPRE2	psi-mi:“MI:0915”(physical association)	0.800
MAPRE2	LMO2	psi-mi:“MI:0915”(physical association)	0.800
LMO2	LDB1	psi-mi:“MI:0915”(physical association)	0.740
MAPRE3	LMO2	psi-mi:“MI:0915”(physical association)	0.740
LDB1	LMO2	psi-mi:“MI:0915”(physical association)	0.740
LMO2	MAPRE3	psi-mi:“MI:0915”(physical association)	0.740
LMO2	SAXO1	psi-mi:“MI:0915”(physical association)	0.670
ZNF24	LMO2	psi-mi:“MI:0915”(physical association)	0.670
HNRNPM	LMO2	psi-mi:“MI:0915”(physical association)	0.670
PRKG1	LMO2	psi-mi:“MI:0915”(physical association)	0.670
LMO2	RINT1	psi-mi:“MI:0915”(physical association)	0.670
PHC2	LMO2	psi-mi:“MI:0915”(physical association)	0.670
ABI2	LMO2	psi-mi:“MI:0915”(physical association)	0.670
SAXO1	LMO2	psi-mi:“MI:0915”(physical association)	0.670
LMO2	PRKG1	psi-mi:“MI:0915”(physical association)	0.670
LMO2	ZNF24	psi-mi:“MI:0915”(physical association)	0.670
LMO2	PHC2	psi-mi:“MI:0915”(physical association)	0.670
LMO2	ABI2	psi-mi:“MI:0915”(physical association)	0.670

BioGRID (372): LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), LMO2 (Two-hybrid), MAGEA8 (Two-hybrid), HNRNPM (Two-hybrid), PDE9A (Two-hybrid), PRKG1 (Two-hybrid)

ESM2 similar proteins: A0A2R8RWN9, A5PKA5, O15294, O89050, P25791, P25801, P48059, P49136, P49139, P49336, P56558, P61201, P61202, P61203, P61968, P61969, P79101, P81436, Q08211, Q1LZ94, Q27HV0, Q28141, Q2KJ33, Q3SWZ8, Q3UHD6, Q5FVB2, Q5M8V8, Q5R874, Q5RB35, Q5SRY7, Q5ZIH0, Q6DJ06, Q7Z4I7, Q801P0, Q8AW92, Q8CGY8, Q8K4V4, Q8R3L8, Q90XH3, Q91854

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
LMO2	“up-regulates quantity by expression”	ANGPT2	“transcriptional regulation”
LMO2	“up-regulates quantity by expression”	ERG	“transcriptional regulation”
LMO2	up-regulates	TAL1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	39
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

504 predictions. Top by Δscore:

Variant	Effect	Δscore
11:33864596:GGGTA:G	donor_loss	1.0000
11:33864597:GGTA:G	donor_loss	1.0000
11:33864598:GTA:G	donor_loss	1.0000
11:33864599:TA:T	donor_loss	1.0000
11:33864600:A:C	donor_loss	1.0000
11:33864816:CC:C	acceptor_gain	1.0000
11:33864816:CCCTG:C	acceptor_loss	1.0000
11:33864817:CC:C	acceptor_gain	1.0000
11:33864817:CCTGG:C	acceptor_loss	1.0000
11:33864818:C:A	acceptor_loss	1.0000
11:33864818:C:CC	acceptor_gain	1.0000
11:33869344:A:AC	donor_gain	1.0000
11:33869345:C:CC	donor_gain	1.0000
11:33869345:CT:C	donor_gain	1.0000
11:33864813:GTTCC:G	acceptor_gain	0.9900
11:33864815:TCC:T	acceptor_gain	0.9900
11:33864816:CCC:C	acceptor_gain	0.9900
11:33869340:ACTT:A	donor_loss	0.9900
11:33869342:TTACT:T	donor_loss	0.9900
11:33869343:TACT:T	donor_loss	0.9900
11:33869344:ACT:A	donor_gain	0.9900
11:33869344:ACTCT:A	donor_loss	0.9900
11:33869345:CTC:C	donor_gain	0.9900
11:33869365:T:TA	donor_gain	0.9900
11:33864627:T:TA	donor_gain	0.9800
11:33864814:TTCC:T	acceptor_gain	0.9800
11:33864814:TTCCC:T	acceptor_gain	0.9800
11:33864815:TCCC:T	acceptor_gain	0.9800
11:33864818:C:T	acceptor_gain	0.9800
11:33866990:A:AC	donor_gain	0.9800

AlphaMissense

1465 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:33859551:G:C	C94W	1.000
11:33859553:A:G	C94R	1.000
11:33864688:G:C	C57W	1.000
11:33864689:C:T	C57Y	1.000
11:33864690:A:G	C57R	1.000
11:33859402:C:G	C144S	0.999
11:33859402:C:T	C144Y	0.999
11:33859403:A:G	C144R	0.999
11:33859403:A:T	C144S	0.999
11:33859438:C:A	G132V	0.999
11:33859438:C:T	G132D	0.999
11:33859439:C:G	G132R	0.999
11:33859447:A:G	F129S	0.999
11:33859458:A:C	C125W	0.999
11:33859459:C:T	C125Y	0.999
11:33859467:G:C	C122W	0.999
11:33859468:C:G	C122S	0.999
11:33859469:A:G	C122R	0.999
11:33859469:A:T	C122S	0.999
11:33859473:G:C	F120L	0.999
11:33859473:G:T	F120L	0.999
11:33859474:A:G	F120S	0.999
11:33859475:A:G	F120L	0.999
11:33859476:A:C	C119W	0.999
11:33859477:C:G	C119S	0.999
11:33859478:A:G	C119R	0.999
11:33859478:A:T	C119S	0.999
11:33859485:G:C	H116Q	0.999
11:33859485:G:T	H116Q	0.999
11:33859487:G:C	H116D	0.999

dbSNP variants (sampled 300 via entrez): RS1000025412 (11:33864043 C>G), RS1000109210 (11:33892009 G>C), RS1000306348 (11:33877621 C>T), RS1000385660 (11:33864410 G>C), RS1000419347 (11:33882095 C>T), RS1000486681 (11:33884162 C>A), RS1000547299 (11:33876126 C>T), RS1000568936 (11:33870971 T>A,C), RS1000642065 (11:33875770 A>G), RS1000711231 (11:33890492 C>A,T), RS1000757554 (11:33883845 G>A,T), RS1000821380 (11:33883924 C>G), RS1000954731 (11:33869283 C>A,T), RS1000981654 (11:33888820 C>G), RS1001082056 (11:33870321 C>A,G)

Disease associations

OMIM: gene MIM:180385 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

13 associations (top):

Study	Trait	p-value
GCST000477_52	Cognitive performance	8.000000e-06
GCST004601_156	Red blood cell count	3.000000e-10
GCST004602_194	Mean corpuscular volume	2.000000e-16
GCST004630_248	Mean corpuscular hemoglobin	2.000000e-19
GCST012305_12	Major depressive disorder x sex interaction	6.000000e-06
GCST90002381_296	Eosinophil count	1.000000e-11
GCST90002382_380	Eosinophil percentage of white cells	7.000000e-11
GCST90002390_27	Mean corpuscular hemoglobin	9.000000e-42
GCST90002392_567	Mean corpuscular volume	2.000000e-40
GCST90002393_225	Monocyte count	2.000000e-09
GCST90002396_463	Mean reticulocyte volume	2.000000e-35
GCST90002397_522	Mean spheric corpuscular volume	2.000000e-33
GCST90002403_199	Red blood cell count	1.000000e-30

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0003926	neuropsychological test
EFO:0004305	erythrocyte count
EFO:0004527	mean corpuscular hemoglobin
EFO:0008343	sex interaction measurement
EFO:0004842	eosinophil count
EFO:0007991	eosinophil percentage of leukocytes
EFO:0005091	monocyte count
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL3217402 (SINGLE PROTEIN)

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

ChEMBL bioactivities

1 potent at pChembl≥5 of 1 total, top 1 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
7.54	Kd	29	nM	CHEMBL3220079

CTD chemical–gene interactions

46 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	increases methylation, affects expression, decreases expression, decreases methylation, increases expression	4
(+)-JQ1 compound	decreases expression, increases expression	3
Tretinoin	decreases expression, increases expression	3
Valproic Acid	affects expression, decreases expression	3
sodium arsenite	affects methylation, increases expression	2
belinostat	decreases expression, affects cotreatment	2
Panobinostat	affects cotreatment, decreases expression	2
Estradiol	affects expression, affects cotreatment, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
methyleugenol	increases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	increases expression	1
bisphenol A	decreases methylation	1
deoxynivalenol	decreases expression	1
2,5,2’,5’-tetrachlorobiphenyl	increases expression	1
trichostatin A	increases expression, decreases expression	1
butyraldehyde	increases expression	1
perfluorooctanoic acid	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
pentanal	increases expression	1
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
pomalidomide	decreases expression	1
2,2’,4,4’,5-brominated diphenyl ether	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
MRK 003	decreases expression	1
NSC668394	increases expression	1
Temozolomide	decreases expression	1
Decitabine	affects expression	1
Arsenic Trioxide	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3223526	Binding	Binding affinity to GST-tagged LMO2 (unknown origin) by surface plasmon resonance analysis	Peptides: minimal drug surrogates to interrogate and interfere with protein function — Medchemcomm

Cellosaurus cell lines

4 cell lines: 3 embryonic stem cell, 1 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_A3Y0	SEES3-1V human LMO2, clone1	Embryonic stem cell	Male
CVCL_A3Y1	SEES3-1V human LMO2, clone2	Embryonic stem cell	Male
CVCL_A3Y2	SEES3-1V human LMO2, clone3	Embryonic stem cell	Male
CVCL_B1GA	Abcam A-549 LMO2 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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