TLR1

toll like receptor 1, the group of CD molecules|Toll like receptors

Basic information

Region (hg38): 4:38787555-38856817

Links

ENSG00000174125 ∙ NCBI:7096 ∙ OMIM:601194 ∙ HGNC:11847 ∙ Uniprot:Q15399 ∙ 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 TLR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLR1 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				12	4	16
missense			40	10	8	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	40	22	12

Variants in TLR1

This is a list of pathogenic ClinVar variants found in the TLR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-38792853-T-TTATATATATATATATATATATATATATATATA			Uncertain significance (-)
4-38796523-G-C		not specified	Uncertain significance (Jan 31, 2023)
4-38796548-T-C		not specified	Uncertain significance (Aug 30, 2021)
4-38796601-T-C		not specified	Uncertain significance (Sep 22, 2022)
4-38796673-T-G			Likely benign (May 01, 2023)
4-38796683-T-A		not specified	Uncertain significance (Jan 22, 2024)
4-38796685-T-C		not specified	Uncertain significance (Mar 24, 2023)
4-38796695-A-C		not specified	Uncertain significance (Mar 31, 2024)
4-38796740-A-C		not specified	Uncertain significance (Aug 02, 2021)
4-38796760-T-C		not specified	Uncertain significance (Jun 29, 2023)
4-38796778-G-A		not specified	Uncertain significance (Oct 04, 2022)
4-38796796-A-G		Rheumatoid arthritis	Pathogenic (Nov 02, 2020)
4-38796804-G-A			Benign/Likely benign (May 01, 2023)
4-38796812-C-T			not provided (-)
4-38796826-T-C		not specified	Uncertain significance (May 30, 2024)
4-38796880-A-G			not provided (-)
4-38796894-G-A		TLR1-related disorder	Benign (May 15, 2018)
4-38796904-T-A		not specified	Uncertain significance (Dec 09, 2023)
4-38796904-T-C		not specified	Uncertain significance (Aug 12, 2022)
4-38796930-A-G			Likely benign (May 18, 2018)
4-38796974-G-C		not specified	Uncertain significance (Oct 06, 2021)
4-38797027-C-A		Leprosy, protection against • Leprosy, susceptibility to, 1 • TLR1-related disorder	Conflicting classifications of pathogenicity; protective (Jun 10, 2022)
4-38797028-T-C		not specified	Uncertain significance (Mar 25, 2024)
4-38797036-G-A			Uncertain significance (-)
4-38797063-A-G		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLR1	protein_coding	protein_coding	ENST00000308979	1	66141

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.87e-23	0.0000283	125251	2	493	125746	0.00197

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.702	435	396	1.10	0.0000194	5247
Missense in Polyphen		146	122.09	1.1958		1746
Synonymous	-0.827	167	154	1.08	0.00000800	1456
Loss of Function	-1.73	29	20.6	1.41	8.75e-7	318

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00177	0.00177
Ashkenazi Jewish	0.00824	0.00787
East Asian	0.00190	0.00190
Finnish	0.00176	0.00176
European (Non-Finnish)	0.00182	0.00154
Middle Eastern	0.00190	0.00190
South Asian	0.00354	0.00344
Other	0.00295	0.00261

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the innate immune response to microbial agents. Specifically recognizes diacylated and triacylated lipopeptides. Cooperates with TLR2 to mediate the innate immune response to bacterial lipoproteins or lipopeptides (PubMed:21078852). Forms the activation cluster TLR2:TLR1:CD14 in response to triacylated lipopeptides, this cluster triggers signaling from the cell surface and subsequently is targeted to the Golgi in a lipid-raft dependent pathway (PubMed:16880211). Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response. {ECO:0000269|PubMed:16880211, ECO:0000269|PubMed:21078852}.
• Pathway: Toll-like receptor signaling pathway - Homo sapiens (human);Tuberculosis - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;IL1 and megakaryocytes in obesity;Toll-like Receptor Signaling;Simplified Depiction of MYD88 Distinct Input-Output Pathway;Toll-like Receptor Signaling Pathway;Toll-Like Receptors Cascades;Antimicrobial peptides;Innate Immune System;Immune System;Adaptive Immune System;Beta defensins;Antigen processing-Cross presentation;Class I MHC mediated antigen processing & presentation;Defensins;Regulation of TLR by endogenous ligand;ER-Phagosome pathway;Toll Like Receptor 4 (TLR4) Cascade;MyD88:Mal cascade initiated on plasma membrane;Toll Like Receptor TLR1:TLR2 Cascade;Toll Like Receptor TLR6:TLR2 Cascade;Toll Like Receptor 2 (TLR2) Cascade;Endogenous TLR signaling (Consensus)

Recessive Scores

• pRec: 0.354

Intolerance Scores

• loftool: 0.963
• rvis_EVS: 1.32
• rvis_percentile_EVS: 94.07

Haploinsufficiency Scores

• pHI: 0.0760
• hipred: N
• hipred_score: 0.327
• ghis: 0.438

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.210

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlr1
• Phenotype: hematopoietic system phenotype; immune system phenotype

Gene ontology

• Biological process: cell activation;toll-like receptor signaling pathway;MyD88-dependent toll-like receptor signaling pathway;inflammatory response;immune response;signal transduction;toll-like receptor 1 signaling pathway;positive regulation of toll-like receptor 2 signaling pathway;toll-like receptor TLR1:TLR2 signaling pathway;macrophage activation;detection of triacyl bacterial lipopeptide;positive regulation of tumor necrosis factor biosynthetic process;innate immune response;positive regulation of interleukin-6 biosynthetic process;cellular response to triacyl bacterial lipopeptide;positive regulation of interleukin-8 secretion
• Cellular component: Golgi apparatus;plasma membrane;integral component of plasma membrane;membrane;phagocytic vesicle membrane;Toll-like receptor 1-Toll-like receptor 2 protein complex;membrane raft
• Molecular function: transmembrane signaling receptor activity;protein binding;Toll-like receptor 2 binding;signaling receptor activity;identical protein binding;protein heterodimerization activity;lipopeptide binding