TLR7
toll like receptor 7, the group of Toll like receptors
Basic information
Region (hg38): X:12867072-12890361
Links
Phenotypes
GenCC
Source:
- immunodeficiency 74, COVID-19-related, X-linked (Limited), mode of inheritance: Unknown
- systemic lupus erythematosus 17 (Moderate), mode of inheritance: XL
- systemic lupus erythematosus (Supportive), mode of inheritance: Unknown
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 74, COVID-19 related, X-linked | XL | Allergy/Immunology/Infectious | Individuals with Immunodeficiency 74, COVID-19 related, X-linked, may demonstrate susceptibility to severe COVID-19, and awareness may allow preventative measures (such as adhering to practices to reduce the chance of infection); Individuals with Systemic lupus erythematosus have been described as benefiting from medical management (eg, with prednisone, azathioprine, mycophenolate, rituximab, immunoglobulins, Etanercept) | Allergy/Immunology/Infectious | 32706371; 35477763 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (244 variants)
- not_specified (45 variants)
- Systemic_lupus_erythematosus_17 (5 variants)
- TLR7-related_disorder (4 variants)
- Immunodeficiency_74,_COVID-19-related,_X-linked (3 variants)
- Systemic_lupus_erythematosus (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLR7 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016562.4. 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 | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 101 | 10 | 111 | |||
| missense | 144 | 156 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 3 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 5 | 0 | 148 | 106 | 13 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TLR7 | protein_coding | protein_coding | ENST00000380659 | 2 | 23298 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.979 | 0.0209 | 125735 | 4 | 5 | 125744 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.01 | 205 | 368 | 0.558 | 0.0000261 | 6976 |
| Missense in Polyphen | 42 | 127.94 | 0.32828 | 2454 | ||
| Synonymous | -0.527 | 157 | 149 | 1.05 | 0.0000109 | 2020 |
| Loss of Function | 3.80 | 2 | 20.7 | 0.0968 | 0.00000143 | 428 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000113 | 0.0000981 |
| Ashkenazi Jewish | 0.000268 | 0.000198 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000244 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000169 | 0.0000980 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Key component of innate and adaptive immunity. TLRs (Toll-like receptors) control host immune response against pathogens through recognition of molecular patterns specific to microorganisms. TLR7 is a nucleotide-sensing TLR which is activated by single-stranded RNA. Acts via MYD88 and TRAF6, leading to NF-kappa-B activation, cytokine secretion and the inflammatory response (By similarity). {ECO:0000250, ECO:0000269|PubMed:18250417}.;
- Pathway
- Influenza A - Homo sapiens (human);Toll-like receptor signaling pathway - Homo sapiens (human);Measles - Homo sapiens (human);Regulation of toll-like receptor signaling pathway;Toll-like Receptor Signaling;Simplified Depiction of MYD88 Distinct Input-Output Pathway;Toll-like Receptor Signaling Pathway;Toll Like Receptor 7/8 (TLR7/8) Cascade;TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling;toll-like receptor pathway;Toll Like Receptor 9 (TLR9) Cascade;Trafficking and processing of endosomal TLR;Toll-Like Receptors Cascades;Innate Immune System;Immune System;TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation;MyD88 dependent cascade initiated on endosome
(Consensus)
Recessive Scores
- pRec
- 0.287
Intolerance Scores
- loftool
- 0.271
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.85
Haploinsufficiency Scores
- pHI
- 0.134
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.571
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.122
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tlr7
- Phenotype
- cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; renal/urinary 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); hematopoietic system phenotype;
Gene ontology
- Biological process
- microglial cell activation;regulation of protein phosphorylation;toll-like receptor signaling pathway;MyD88-dependent toll-like receptor signaling pathway;immune response;I-kappaB kinase/NF-kappaB signaling;I-kappaB phosphorylation;positive regulation of chemokine production;positive regulation of interleukin-6 production;positive regulation of interleukin-8 production;toll-like receptor 7 signaling pathway;toll-like receptor 9 signaling pathway;positive regulation of interferon-gamma biosynthetic process;innate immune response;positive regulation of interferon-alpha biosynthetic process;positive regulation of interferon-beta biosynthetic process;positive regulation of interleukin-8 biosynthetic process;positive regulation of inflammatory response;defense response to virus;cellular response to mechanical stimulus;positive regulation of NIK/NF-kappaB signaling
- Cellular component
- Golgi membrane;cytoplasm;lysosome;endosome;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;endosome membrane;integral component of membrane;early phagosome;endolysosome membrane;receptor complex
- Molecular function
- double-stranded RNA binding;single-stranded RNA binding;transmembrane signaling receptor activity;drug binding;signaling pattern recognition receptor activity;siRNA binding