LMO7

LIM domain 7, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 13:75620434-75859870

Previous symbols: [ "FBXO20" ]

Links

ENSG00000136153 ∙ NCBI:4008 ∙ OMIM:604362 ∙ HGNC:6646 ∙ Uniprot:Q8WWI1 ∙ 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 LMO7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMO7 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				2	3	5
missense			103	10	3	116
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1		1	2
non coding			1	2		3
Total	0	0	104	14	6

Variants in LMO7

This is a list of pathogenic ClinVar variants found in the LMO7 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-75621746-A-G		not specified	Uncertain significance (Nov 12, 2021)
13-75621795-G-T		not specified	Uncertain significance (Jun 19, 2024)
13-75621805-T-C		not specified	Uncertain significance (May 25, 2022)
13-75621829-G-C		not specified	Uncertain significance (Oct 10, 2023)
13-75621849-C-A		not specified	Likely benign (Sep 13, 2023)
13-75621862-A-G		not specified	Uncertain significance (Apr 18, 2023)
13-75623274-T-C		not specified	Uncertain significance (May 17, 2023)
13-75623309-A-T		not specified	Uncertain significance (Feb 28, 2023)
13-75713213-A-G		not specified	Uncertain significance (Jun 07, 2024)
13-75713222-C-T		not specified	Uncertain significance (Dec 20, 2021)
13-75713256-A-G		LMO7-related disorder	Uncertain significance (Apr 27, 2023)
13-75727054-G-A		not specified	Likely benign (Apr 27, 2022)
13-75727070-A-G		not specified	Uncertain significance (Nov 07, 2022)
13-75727082-C-T		not specified	Uncertain significance (Jul 14, 2021)
13-75727093-G-C		not specified	Uncertain significance (Oct 14, 2023)
13-75800734-C-T			Likely benign (Jun 08, 2018)
13-75800877-G-C		LMO7-related disorder	Uncertain significance (Feb 27, 2024)
13-75804311-G-A			Benign (Mar 05, 2018)
13-75804355-C-T		not specified	Uncertain significance (Dec 22, 2023)
13-75804370-C-T		not specified	Uncertain significance (Jun 02, 2023)
13-75804405-C-T		not specified	Uncertain significance (Oct 12, 2021)
13-75804465-A-G		not specified	Uncertain significance (Jan 18, 2022)
13-75805507-G-A		not specified	Uncertain significance (Jun 09, 2022)
13-75805592-A-G		not specified	Uncertain significance (Feb 28, 2023)
13-75805619-G-A		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMO7	protein_coding	protein_coding	ENST00000465261	23	239435

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000247	1.00	125649	0	99	125748	0.000394

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.168	752	739	1.02	0.0000401	9030
Missense in Polyphen		219	232.96	0.94007		2789
Synonymous	-0.324	269	262	1.03	0.0000138	2638
Loss of Function	5.76	22	76.3	0.288	0.00000409	895

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000805	0.000787
Ashkenazi Jewish	0.00	0.00
East Asian	0.000553	0.000544
Finnish	0.000418	0.000416
European (Non-Finnish)	0.000451	0.000440
Middle Eastern	0.000553	0.000544
South Asian	0.000294	0.000294
Other	0.000502	0.000489

dbNSFP

Source: dbNSFP

• Pathway: Adherens junction - Homo sapiens (human);Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Recessive Scores

• pRec: 0.119

Intolerance Scores

• loftool: 0.945
• rvis_EVS: 0.47
• rvis_percentile_EVS: 78.8

Haploinsufficiency Scores

• pHI: 0.0777
• hipred: N
• hipred_score: 0.354
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.639

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lmo7
• Phenotype: respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); neoplasm; pigmentation 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); vision/eye 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); growth/size/body region phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: lmo7b
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: protein polyubiquitination;protein ubiquitination;regulation of signaling;regulation of cell adhesion;post-translational protein modification;positive regulation of transcription by RNA polymerase II
• Cellular component: ubiquitin ligase complex;nucleus;nuclear envelope;cytoplasm;cytosol;focal adhesion;cell surface;apical plasma membrane
• Molecular function: DNA-binding transcription factor activity;ubiquitin-protein transferase activity;metal ion binding