TLR10

toll like receptor 10, the group of CD molecules|Toll like receptors

Basic information

Region (hg38): 4:38772237-38782990

Links

ENSG00000174123 ∙ NCBI:81793 ∙ OMIM:606270 ∙ HGNC:15634 ∙ Uniprot:Q9BXR5 ∙ 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 TLR10 gene.

• Inborn genetic diseases (27 variants)
• not provided (8 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLR10 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					4	4
missense			27	3		30
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	3	5

Variants in TLR10

This is a list of pathogenic ClinVar variants found in the TLR10 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-38773183-A-T		not specified	Uncertain significance (Jan 18, 2023)
4-38773195-C-T			Likely benign (Dec 01, 2022)
4-38773250-C-T		not specified	Uncertain significance (Aug 02, 2022)
4-38773259-T-C		not specified	Uncertain significance (Oct 02, 2023)
4-38773274-C-T		not specified	Uncertain significance (Sep 16, 2021)
4-38773286-C-T		not specified	Uncertain significance (Oct 12, 2022)
4-38773336-T-C			Likely benign (Jul 17, 2018)
4-38773373-T-C		not specified	Uncertain significance (Jun 02, 2023)
4-38773408-A-G		not specified	Uncertain significance (Nov 05, 2021)
4-38773418-T-C		not specified	Uncertain significance (Mar 06, 2023)
4-38773422-A-T		not specified	Uncertain significance (Oct 14, 2023)
4-38773592-G-A		not specified	Uncertain significance (Jun 11, 2021)
4-38773760-C-G		not specified	Uncertain significance (Jan 25, 2023)
4-38773784-G-A			Benign (Dec 31, 2019)
4-38773881-G-A			Benign (Jun 06, 2018)
4-38774011-G-A		not specified	Uncertain significance (Oct 29, 2021)
4-38774035-G-T		not specified	Uncertain significance (Dec 06, 2021)
4-38774041-A-T		not specified	Uncertain significance (Feb 21, 2024)
4-38774085-G-A			Benign (Jul 17, 2018)
4-38774320-A-G		not specified	Uncertain significance (Dec 18, 2023)
4-38774399-G-C		not specified	Uncertain significance (Nov 03, 2022)
4-38774459-T-C		not specified	Uncertain significance (Sep 26, 2023)
4-38774483-G-A			Benign (Dec 31, 2019)
4-38774485-A-G		not specified	Uncertain significance (Oct 20, 2021)
4-38774599-A-G		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLR10	protein_coding	protein_coding	ENST00000308973	1	10752

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.48e-9	0.773	125124	6	612	125742	0.00246

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.237	391	404	0.967	0.0000192	5370
Missense in Polyphen		95	97.076	0.97861		1449
Synonymous	3.10	103	152	0.679	0.00000741	1503
Loss of Function	1.50	17	25.1	0.677	0.00000143	332

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0233	0.0230
Ashkenazi Jewish	0.00199	0.00189
East Asian	0.00111	0.00109
Finnish	0.00	0.00
European (Non-Finnish)	0.000812	0.000783
Middle Eastern	0.00111	0.00109
South Asian	0.00251	0.00229
Other	0.00309	0.00294

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the innate immune response to microbial agents. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response (By similarity). {ECO:0000250}.
• Pathway: Simplified Depiction of MYD88 Distinct Input-Output 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: 0.217

Intolerance Scores

• loftool: 0.285
• rvis_EVS: 2.32
• rvis_percentile_EVS: 98.36

Haploinsufficiency Scores

• pHI: 0.0888
• hipred: N
• hipred_score: 0.133
• ghis: 0.449

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.333

Gene Damage Prediction

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

Gene ontology

• Biological process: toll-like receptor signaling pathway;MyD88-dependent toll-like receptor signaling pathway;inflammatory response;immune response;toll-like receptor 10 signaling pathway;innate immune response;regulation of cytokine secretion;positive regulation of inflammatory response
• Cellular component: plasma membrane;integral component of plasma membrane;membrane
• Molecular function: transmembrane signaling receptor activity;protein binding;identical protein binding