LMO3

protein-coding

LIM domain only 3, the group of LIM domain containing

Gene summary

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. [provided by RefSeq, Aug 2011]

Previous symbols:

RBTNL2

MANE transcript

NM_018640.5

Inheritance

—

ClinVar variants

U:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.12

Max pathogenic AF

—

Genomic locus

chr12:16,548,372-16,610,594

External References & Databases

Ensembl (ENSG00000048540)

Transcript & Mutation Effects

hg38 • Region Span ~62.2 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LMO3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 9

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_018640.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	10	0	0	10

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 126 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_018640.5	RefSeq	NP_061110.2	3	MANE Select
ENST00000537304.6	Ensembl	ENSP00000440099.1	3	MANE Select
NM_001001395.2	RefSeq	NP_001001395.1	3	Standard
NM_001243609.1	RefSeq	NP_001230538.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of peroxisome proliferator activated receptor signaling pathway
positive regulation of fat cell differentiation
negative regulation of ERK1 and ERK2 cascade
positive regulation of glucocorticoid receptor signaling pathway

Molecular Function

protein binding
metal ion binding

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000540445
Coding exons: 4
Length: 62222
Individuals with no LoFs: 125717
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125718
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.01	41	96.5	0.425	0.00000525	1104
Missense (PolyPhen)		8	35.905	0.22281		402
Synonymous	0.206	32	33.5	0.955	0.00000186	296
Loss of Function	2.36	1	8.34	0.120	4.36e-7	101

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.118

Intolerance Scores

LoFtool: 0.209
RVIS EVS: 0.04
RVIS percentile EVS: 56.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.666

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low