chr4:38797027:C>A Detail (hg38) (TLR1)

Information

Genome

Assembly Position
hg19 chr4:38,798,648-38,798,648 View the variant detail on this assembly version.
hg38 chr4:38,797,027-38,797,027

HGVS

Type Transcript Protein
RefSeq NM_003263.3:c.1805G>T NP_003254.2:p.Ser602Ile
Ensemble ENST00000308979.7:c.1805G>T ENST00000308979.7:p.Ser602Ile
ENST00000502213.6:c.1805G>T ENST00000502213.6:p.Ser602Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.988
ToMMo:0.989
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.990

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601194 OMIM
HGNC 11847 HGNC
Ensembl ENSG00000174125 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv16719477 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
protective 2012-12-01 no assertion criteria provided Leprosy, protection against germline Detail
Uncertain risk allele 2022-06-10 no assertion criteria provided Leprosy, susceptibility to, 1 inherited Detail
Benign 2019-10-17 criteria provided, single submitter TLR1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.015 Tuberculosis, Pulmonary In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile... BeFree 20797905 Detail
<0.001 Tuberculosis, Pulmonary In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile... BeFree 20797905 Detail
0.012 Tuberculosis, Pulmonary In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile... BeFree 20797905 Detail
0.002 Tuberculosis, Pulmonary In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile... BeFree 20797905 Detail
0.001 Tuberculosis, Pulmonary In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile... BeFree 20797905 Detail
<0.001 gastric ulcer The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ul... BeFree 23067142 Detail
<0.001 Malignant neoplasm of stomach The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ul... BeFree 23067142 Detail
<0.001 leptospirosis Association of Toll-like receptor 2 Arg753Gln and Toll-like receptor 1 Ile602Ser... BeFree 25784560 Detail
0.001 Tuberculosis, Pulmonary The aim of this study was to investigate whether the functional genetic variatio... BeFree 20650298 Detail
0.006 Lyme disease The aim of the present study was to investigate the Arg753Gln single-nucleotide ... BeFree 25784560 Detail
0.001 Tuberculosis, Pulmonary Human toll-like receptor 1 T1805G polymorphism and susceptibility to pulmonary t... BeFree 23575331 Detail
0.007 tuberculosis In addition, after stimulated with inactivated lysate of M. tuberculosis strain ... BeFree 25544311 Detail
0.010 Lyme disease The aim of the present study was to investigate the Arg753Gln single-nucleotide ... BeFree 25784560 Detail
<0.001 Asymptomatic Infections Genotype distributions for the TLR-1 I602S differed significantly between patien... BeFree 18662133 Detail
0.003 Dermatitis, Atopic In this study, we demonstrated that TLR1 rs5743618 was associated with asthma an... BeFree 24445834 Detail
0.001 Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site TLR1 1805T/G showed statistical differences when the control (Hp-) and infected ... BeFree 24754375 Detail
<0.001 bronchiolitis In this study, we demonstrated that TLR1 rs5743618 was associated with asthma an... BeFree 24445834 Detail
0.130 asthma In this study, we demonstrated that TLR1 rs5743618 was associated with asthma an... BeFree 24445834 Detail
0.011 tuberculosis In addition, after stimulated with inactivated lysate of M. tuberculosis strain ... BeFree 25544311 Detail
<0.001 stomach carcinoma The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ul... BeFree 23067142 Detail
<0.001 leptospirosis Association of Toll-like receptor 2 Arg753Gln and Toll-like receptor 1 Ile602Ser... BeFree 25784560 Detail
0.006 tuberculosis Toll-like receptor 1(TLR1) Gene SNP rs5743618 is associated with increased risk ... BeFree 25544311 Detail
0.015 Tuberculosis, Pulmonary The aim of this study was to investigate whether the functional genetic variatio... BeFree 20650298 Detail
<0.001 Ileal Diseases In CD, we found a negative association between ileal disease involvement and TLR... BeFree 16374251 Detail
0.064 tuberculosis In addition, after stimulated with inactivated lysate of M. tuberculosis strain ... BeFree 25544311 Detail
<0.001 leprosy We have conducted an association analysis of more than 1,500 individuals from di... BeFree 20617178 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003263.4(TLR1):c.1805G>T (p.Ser602Ile) AND Leprosy, protection against ClinVar Detail
NM_003263.4(TLR1):c.1805G>T (p.Ser602Ile) AND Leprosy, susceptibility to, 1 ClinVar Detail
NM_003263.4(TLR1):c.1805G>T (p.Ser602Ile) AND TLR1-related disorder ClinVar Detail
In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile602Ser), TLR-2 2258G... DisGeNET Detail
In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile602Ser), TLR-2 2258G... DisGeNET Detail
In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile602Ser), TLR-2 2258G... DisGeNET Detail
In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile602Ser), TLR-2 2258G... DisGeNET Detail
In the present study, we investigated whether variants in the TLR-1 1805T/G (Ile602Ser), TLR-2 2258G... DisGeNET Detail
The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ulcer (p = .051). DisGeNET Detail
The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ulcer (p = .051). DisGeNET Detail
Association of Toll-like receptor 2 Arg753Gln and Toll-like receptor 1 Ile602Ser single-nucleotide p... DisGeNET Detail
The aim of this study was to investigate whether the functional genetic variations at position 1805 ... DisGeNET Detail
The aim of the present study was to investigate the Arg753Gln single-nucleotide polymorphism (SNP) o... DisGeNET Detail
Human toll-like receptor 1 T1805G polymorphism and susceptibility to pulmonary tuberculosis in north... DisGeNET Detail
In addition, after stimulated with inactivated lysate of M. tuberculosis strain H37Rv, samples of pe... DisGeNET Detail
The aim of the present study was to investigate the Arg753Gln single-nucleotide polymorphism (SNP) o... DisGeNET Detail
Genotype distributions for the TLR-1 I602S differed significantly between patients with mild malaria... DisGeNET Detail
In this study, we demonstrated that TLR1 rs5743618 was associated with asthma and atopic eczema duri... DisGeNET Detail
TLR1 1805T/G showed statistical differences when the control (Hp-) and infected (Hp+) groups (P = 0.... DisGeNET Detail
In this study, we demonstrated that TLR1 rs5743618 was associated with asthma and atopic eczema duri... DisGeNET Detail
In this study, we demonstrated that TLR1 rs5743618 was associated with asthma and atopic eczema duri... DisGeNET Detail
In addition, after stimulated with inactivated lysate of M. tuberculosis strain H37Rv, samples of pe... DisGeNET Detail
The TLR1 I602S SNP is significantly associated with GC (p = .002) and gastric ulcer (p = .051). DisGeNET Detail
Association of Toll-like receptor 2 Arg753Gln and Toll-like receptor 1 Ile602Ser single-nucleotide p... DisGeNET Detail
Toll-like receptor 1(TLR1) Gene SNP rs5743618 is associated with increased risk for tuberculosis in ... DisGeNET Detail
The aim of this study was to investigate whether the functional genetic variations at position 1805 ... DisGeNET Detail
In CD, we found a negative association between ileal disease involvement and TLR1 S602I (P = .03, OR... DisGeNET Detail
In addition, after stimulated with inactivated lysate of M. tuberculosis strain H37Rv, samples of pe... DisGeNET Detail
We have conducted an association analysis of more than 1,500 individuals from different case-control... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs5743618 dbSNP
Genome
hg38
Position
chr4:38,797,027-38,797,027
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
VQSRTrancheSNP99.00to99.90
# of samples (HGVD)
1098
Mean of sample read depth (HGVD)
54.29
Standard deviation of sample read depth (HGVD)
27.18
Number of reference allele (HGVD)
27
Number of alternative allele (HGVD)
2169
Allele Frequency (HGVD)
0.9877049180327869
Gene Symbol (HGVD)
TLR1
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs5743618
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.989
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16575
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
8563
East Asian Heterozygous Counts (ExAC)
87
East Asian Homozygous Counts (ExAC)
4238
East Asian Allele Frequency (ExAC)
0.9899421965317919
Chromosome Counts in All Race (ExAC)
121302
Allele Counts in All Race (ExAC)
65372
Heterozygous Counts in All Race (ExAC)
19500
Homozygous Counts in All Race (ExAC)
22936
Allele Frequency in All Race (ExAC)
0.5389193912713722
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