TLR5

toll like receptor 5, the group of Toll like receptors

Basic information

Region (hg38): 1:223109404-223143292

Previous symbols: [ "SLEB1" ]

Links

ENSG00000187554 ∙ NCBI:7100 ∙ OMIM:603031 ∙ HGNC:11851 ∙ Uniprot:O60602 ∙ 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 TLR5 gene.

• not_specified (95 variants)
• not_provided (15 variants)
• TLR5-related_disorder (3 variants)
• Systemic_lupus_erythematosus,_susceptibility_to,_1 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLR5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003268.6. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	3	7
missense			82	15	3	100
nonsense						0
start loss						0
frameshift		1				1
splice donor/acceptor (+/-2bp)						0
Total	0	1	82	19	6

Highest pathogenic variant AF is 6.840488e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLR5	protein_coding	protein_coding	ENST00000540964	1	33877

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.48e-13	0.0359	112631	459	12658	125748	0.0536

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.392	407	430	0.947	0.0000215	5688
Missense in Polyphen		102	117.92	0.86498		1695
Synonymous	-0.326	178	173	1.03	0.00000884	1683
Loss of Function	0.206	20	21.0	0.951	0.00000109	289

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0481	0.0480
Ashkenazi Jewish	0.0286	0.0286
East Asian	0.0282	0.0282
Finnish	0.0465	0.0467
European (Non-Finnish)	0.0625	0.0623
Middle Eastern	0.0282	0.0282
South Asian	0.104	0.103
Other	0.0504	0.0506

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the innate immune response to microbial agents. Mediates detection of bacterial flagellins. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. {ECO:0000269|PubMed:11323673}.
• Disease: DISEASE: Systemic lupus erythematosus 1 (SLEB1) [MIM:601744]: A chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.
• Pathway: Salmonella infection - Homo sapiens (human);Legionellosis - Homo sapiens (human);Inflammatory bowel disease (IBD) - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Pathogenic Escherichia coli infection;Toll-like Receptor Signaling;Simplified Depiction of MYD88 Distinct Input-Output Pathway;Toll-like Receptor Signaling Pathway;MyD88 cascade initiated on plasma membrane;Toll Like Receptor 10 (TLR10) Cascade;Toll Like Receptor 5 (TLR5) Cascade;Toll-Like Receptors Cascades;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.266

Intolerance Scores

• loftool: 0.654
• rvis_EVS: 1.65
• rvis_percentile_EVS: 96.21

Haploinsufficiency Scores

• pHI: 0.0769
• hipred: N
• hipred_score: 0.123
• ghis: 0.400

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.974

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlr5
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system 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); digestive/alimentary phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype

Gene ontology

• Biological process: MyD88-dependent toll-like receptor signaling pathway;inflammatory response;positive regulation of interleukin-8 production;positive regulation of toll-like receptor signaling pathway;toll-like receptor 5 signaling pathway;defense response to bacterium;innate immune response;regulation of cytokine secretion;cellular response to mechanical stimulus
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: transmembrane signaling receptor activity;interleukin-1 receptor binding