chr4:186083063:C>T Detail (hg38) (TLR3)

Information

Genome

Assembly Position
hg19 chr4:187,004,217-187,004,217 View the variant detail on this assembly version.
hg38 chr4:186,083,063-186,083,063

HGVS

Type Transcript Protein
RefSeq NM_003265.2:c.1377C>T NP_003256.1:p.Phe459=
Ensemble ENST00000296795.8:c.1377C>T ENST00000296795.8:p.Phe459=
ENST00000504367.1:c.546C>T ENST00000504367.1:p.Phe182=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.390
ToMMo:0.400
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.328

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 603029 OMIM
HGNC 11849 HGNC
Ensembl ENSG00000164342 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv19855884 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2024-02-01 criteria provided, single submitter Herpes simplex encephalitis, susceptibility to, 1 germline Detail
Benign 2020-10-28 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 hepatitis B To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like recep... BeFree 25388852 Detail
0.002 hepatitis B To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like recep... BeFree 25388852 Detail
0.005 liver carcinoma The results indicated that genetic variant in TLR3 gene rs3775290 polymorphisms ... BeFree 26024592 Detail
0.007 Malignant neoplasm of urinary bladder We examined the association between candidate disease-susceptibility polymorphis... BeFree 23142523 Detail
<0.001 liver cirrhosis Association analysis showed that the TT genotype of TLR3 rs3775290 was associate... BeFree 26024592 Detail
<0.001 Carcinoma of bladder We examined the association between candidate disease-susceptibility polymorphis... BeFree 23142523 Detail
0.002 stomach carcinoma The TLR3 gene (c. 1377C/T) polymorphisms and the del allele of the TLR2 gene ( 1... BeFree 25843196 Detail
<0.001 Malignant neoplasm of urinary bladder We examined the association between candidate disease-susceptibility polymorphis... BeFree 23142523 Detail
0.002 Carcinoma of bladder We examined the association between candidate disease-susceptibility polymorphis... BeFree 23142523 Detail
<0.001 stomach carcinoma The TLR3 gene (c. 1377C/T) polymorphisms and the del allele of the TLR2 gene ( 1... BeFree 25843196 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003265.3(TLR3):c.1377C>T (p.Phe459=) AND not specified ClinVar Detail
NM_003265.3(TLR3):c.1377C>T (p.Phe459=) AND Herpes simplex encephalitis, susceptibility to, 1 ClinVar Detail
NM_003265.3(TLR3):c.1377C>T (p.Phe459=) AND not provided ClinVar Detail
To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs) 3 and 9 ... DisGeNET Detail
To investigate whether single nucleotide polymorphisms (SNPs) in Toll-like receptors (TLRs) 3 and 9 ... DisGeNET Detail
The results indicated that genetic variant in TLR3 gene rs3775290 polymorphisms may be a protective ... DisGeNET Detail
We examined the association between candidate disease-susceptibility polymorphisms in the single nuc... DisGeNET Detail
Association analysis showed that the TT genotype of TLR3 rs3775290 was associated with a decreased r... DisGeNET Detail
We examined the association between candidate disease-susceptibility polymorphisms in the single nuc... DisGeNET Detail
The TLR3 gene (c. 1377C/T) polymorphisms and the del allele of the TLR2 gene ( 196 to 174) were both... DisGeNET Detail
We examined the association between candidate disease-susceptibility polymorphisms in the single nuc... DisGeNET Detail
We examined the association between candidate disease-susceptibility polymorphisms in the single nuc... DisGeNET Detail
The TLR3 gene (c. 1377C/T) polymorphisms and the del allele of the TLR2 gene ( 196 to 174) were both... 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
rs3775290 dbSNP
Genome
hg38
Position
chr4:186,083,063-186,083,063
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1182
Mean of sample read depth (HGVD)
103.58
Standard deviation of sample read depth (HGVD)
47.67
Number of reference allele (HGVD)
1443
Number of alternative allele (HGVD)
921
Allele Frequency (HGVD)
0.3895939086294416
Gene Symbol (HGVD)
TLR3
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))
rs3775290
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3996
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6697
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
2833
East Asian Heterozygous Counts (ExAC)
1943
East Asian Homozygous Counts (ExAC)
445
East Asian Allele Frequency (ExAC)
0.3277417862100879
Chromosome Counts in All Race (ExAC)
121038
Allele Counts in All Race (ExAC)
36399
Heterozygous Counts in All Race (ExAC)
25183
Homozygous Counts in All Race (ExAC)
5608
Allele Frequency in All Race (ExAC)
0.3007237396520101
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