LMO2

LIM domain only 2, the group of LIM domain containing

Basic information

Region (hg38): 11:33858575-33892076

Previous symbols: [ "RBTNL1" ]

Links

ENSG00000135363 ∙ NCBI:4005 ∙ OMIM:180385 ∙ HGNC:6642 ∙ Uniprot:P25791 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMO2 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMO2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	1

Variants in LMO2

This is a list of pathogenic ClinVar variants found in the LMO2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-33859409-T-C		not specified	Uncertain significance (Nov 16, 2022)
11-33859497-G-A			Benign (Feb 08, 2018)
11-33859550-C-A		not specified	Uncertain significance (Dec 02, 2022)
11-33859556-G-A		not specified	Uncertain significance (Dec 08, 2023)
11-33864672-G-A		not specified	Uncertain significance (Jul 06, 2021)
11-33864692-C-T		not specified	Uncertain significance (Oct 14, 2023)
11-33864740-C-T		not specified	Uncertain significance (Aug 09, 2021)
11-33864812-G-A		not specified	Uncertain significance (Dec 17, 2023)
11-33869374-T-G		not specified	Uncertain significance (Feb 10, 2023)
11-33869466-C-T		not specified	Uncertain significance (Nov 27, 2023)
11-33869503-C-T		not specified	Uncertain significance (Feb 27, 2024)
11-33869542-C-G		not specified	Likely benign (Apr 07, 2023)
11-33869563-G-C		not specified	Uncertain significance (Jan 23, 2024)
11-33869569-G-A		not specified	Uncertain significance (Jun 21, 2023)
11-33869580-G-A		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMO2	protein_coding	protein_coding	ENST00000257818	4	33715

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.159	0.781	125737	0	8	125745	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.34	60	97.3	0.616	0.00000649	1443
Missense in Polyphen		26	40.586	0.64061		454
Synonymous	0.365	36	38.9	0.925	0.00000266	463
Loss of Function	1.54	2	6.11	0.327	2.59e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000441	0.0000440
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts with TAL1/SCL to regulate red blood cell development. Also acts with LDB1 to maintain erythroid precursors in an immature state.
• Disease: DISEASE: Note=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.
• Pathway: Transcriptional misregulation in cancer - Homo sapiens (human);Hematopoietic Stem Cell Differentiation;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;RUNX1 regulates transcription of genes involved in differentiation of HSCs;Transcriptional regulation by RUNX1 (Consensus)

Recessive Scores

• pRec: 0.388

Haploinsufficiency Scores

• pHI: 0.916
• hipred: Y
• hipred_score: 0.615
• ghis: 0.510

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.806

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Lmo2
• Phenotype: neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); liver/biliary system phenotype; embryo phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: lmo2
• Affected structure: nucleate erythrocyte
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: multicellular organism development;mRNA transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;cellular response to thyroid hormone stimulus;regulation of hematopoietic stem cell differentiation
• Cellular component: nucleoplasm;transcription factor complex
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II activating transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;bHLH transcription factor binding;metal ion binding;cofactor binding;E-box binding