LMO4

LIM domain only 4, the group of LIM domain containing

Basic information

Region (hg38): 1:87328880-87348923

Links

ENSG00000143013

∙ NCBI:8543 ∙ OMIM:603129 ∙ HGNC:6644 ∙ Uniprot:P61968 ∙ 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 LMO4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMO4 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			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in LMO4

This is a list of pathogenic ClinVar variants found in the LMO4 region.

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

Position	Phenotype	Significance	ClinVar
1-87332106-G-T	not specified	Uncertain significance (Apr 13, 2022)	2283946
1-87332215-A-G	not specified	Uncertain significance (Oct 04, 2022)	2316917
1-87332247-A-G	not specified	Uncertain significance (Oct 29, 2021)	2258142
1-87339616-A-G	not specified	Uncertain significance (May 24, 2023)	2507629
1-87340069-G-A	not specified	Uncertain significance (Sep 14, 2022)	3119357
1-87340153-A-G	not specified	Uncertain significance (Jun 16, 2023)	2596961
1-87340180-A-G	not specified	Uncertain significance (Mar 19, 2024)	3290978

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMO4	protein_coding	protein_coding	ENST00000370544	4	20456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.677	0.319	125683	0	1	125684	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.10	43	103	0.418	0.00000555	1086
Missense in Polyphen		9	38.813	0.23188		415
Synonymous	-0.899	51	43.5	1.17	0.00000257	316
Loss of Function	2.29	1	7.97	0.125	3.39e-7	93

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	0.00	0.00
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Probable transcriptional factor. {ECO:0000250}.;
Pathway: SHP2 signaling;Validated nuclear estrogen receptor alpha network;IL6-mediated signaling events (Consensus)

Recessive Scores

pRec: 0.123

Intolerance Scores

loftool
rvis_EVS: -0.25
rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

pHI: 0.442
hipred: Y
hipred_score: 0.806
ghis: 0.618

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.185

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lmo4
Phenotype: craniofacial phenotype; growth/size/body region phenotype; 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); 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); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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);

Zebrafish Information Network

Gene name: lmo4a
Affected structure: nucleate erythrocyte
Phenotype tag: abnormal
Phenotype quality: decreased amount

Gene ontology

Biological process: neural tube closure;ventricular septum development;transcription by RNA polymerase II;ventral spinal cord interneuron differentiation;spinal cord motor neuron differentiation;spinal cord association neuron differentiation;regulation of cell migration;negative regulation of protein complex assembly;positive regulation of kinase activity;regulation of cell fate specification;positive regulation of transcription by RNA polymerase II;thymus development;regulation of cell activation
Cellular component: transcription factor complex;cell leading edge
Molecular function: enhancer sequence-specific DNA binding;DNA-binding transcription factor activity;protein binding;transcription factor binding;metal ion binding