LMO1

LIM domain only 1, the group of LIM domain containing

Basic information

Region (hg38): 11:8224308-8268716

Previous symbols: [ "RBTN1" ]

Links

ENSG00000166407 ∙ NCBI:4004 ∙ OMIM:186921 ∙ HGNC:6641 ∙ Uniprot:P25800 ∙ 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 LMO1 gene.

• Inborn genetic diseases (4 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMO1 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in LMO1

This is a list of pathogenic ClinVar variants found in the LMO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8224638-G-A		not specified	Uncertain significance (Mar 24, 2023)
11-8224702-A-T		not specified	Uncertain significance (Sep 16, 2021)
11-8230352-C-T		not specified	Uncertain significance (Dec 06, 2022)
11-8230412-A-C		not specified	Uncertain significance (Aug 10, 2023)
11-8230484-G-T		not specified	Uncertain significance (Jan 12, 2024)
11-8233861-C-A		LIM DOMAIN ONLY-1 POLYMORPHISM	Benign (Feb 05, 2016)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMO1	protein_coding	protein_coding	ENST00000335790	4	44413

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.635	0.358	124579	0	1	124580	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	86	96.5	0.892	0.00000609	1029
Missense in Polyphen		34	47.957	0.70897		505
Synonymous	-0.277	41	38.8	1.06	0.00000250	272
Loss of Function	2.20	1	7.49	0.133	4.02e-7	92

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors. {ECO:0000269|PubMed:1703797}.
• Pathway: 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: 0.156

Intolerance Scores

• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.25

Haploinsufficiency Scores

• pHI: 0.784
• hipred: Y
• hipred_score: 0.558
• ghis: 0.566

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.705

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmo1
• 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: negative regulation of transcription by RNA polymerase II;positive regulation of transcription by RNA polymerase II;regulation of T cell homeostatic proliferation;regulation of hematopoietic stem cell differentiation
• Cellular component: nucleus;nucleoplasm
• Molecular function: protein binding;metal ion binding