LMO3

LIM domain only 3, the group of LIM domain containing

Basic information

Region (hg38): 12:16548372-16610594

Previous symbols: [ "RBTNL2" ]

Links

ENSG00000048540 ∙ NCBI:55885 ∙ OMIM:180386 ∙ HGNC:6643 ∙ Uniprot:Q8TAP4 ∙ 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 LMO3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMO3 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	3	1	0

Variants in LMO3

This is a list of pathogenic ClinVar variants found in the LMO3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-16551238-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-16594154-T-C			Likely benign (Jun 05, 2018)
12-16600827-C-T		not specified	Uncertain significance (Dec 15, 2023)
12-16600832-G-A		not specified	Uncertain significance (Jun 22, 2024)
12-16600847-T-C		not specified	Uncertain significance (Dec 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMO3	protein_coding	protein_coding	ENST00000540445	4	62222

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.707	0.290	125717	0	1	125718	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.01	41	96.5	0.425	0.00000525	1104
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.118

Intolerance Scores

• loftool: 0.209
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.25

Haploinsufficiency Scores

• pHI: 0.630
• hipred: Y
• hipred_score: 0.538
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.666

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmo3
• Phenotype: 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); normal phenotype

Gene ontology

• 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
• Cellular component: cytoplasm
• Molecular function: protein binding;metal ion binding