chr7:30452621:C>T Detail (hg38) (NOD1)

Information

Genome

Assembly Position
hg19 chr7:30,492,237-30,492,237 View the variant detail on this assembly version.
hg38 chr7:30,452,621-30,452,621

HGVS

Type Transcript Protein
RefSeq NM_006092.2:c.796G>A NP_006083.1:p.Glu266Lys
Ensemble ENST00000222823.9:c.796G>A ENST00000222823.9:p.Glu266Lys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.464
ToMMo:0.456
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.350

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605980 OMIM
HGNC 16390 HGNC
Ensembl ENSG00000106100 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv28788084 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2021-04-14 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.014 Inflammatory Bowel Diseases The aim of this study was to investigate polymorphisms in the NOD2/CARD15 (R702W... BeFree 16741608 Detail
0.397 Inflammatory Bowel Diseases The aim of this study was to investigate polymorphisms in the NOD2/CARD15 (R702W... BeFree 16741608 Detail
0.017 Crohn Disease NOD1 gene E266K polymorphism is associated with disease susceptibility but not w... BeFree 17964870 Detail
0.003 Cerebrovascular accident Polymorphism in NOD1 G796A alone did not prove to be a risk factor for stroke in... BeFree 19538217 Detail
<0.001 Peptic Ulcer E266K CARD4/NOD1, but not the TLR4 gene polymorphism increases the risk of pepti... BeFree 17309748 Detail
<0.001 Peptic Ulcer E266K CARD4/NOD1, but not the TLR4 gene polymorphism increases the risk of pepti... BeFree 17309748 Detail
0.560 Crohn Disease NOD1 gene E266K polymorphism is associated with disease susceptibility but not w... BeFree 17964870 Detail
<0.001 Chronic gastritis Carriage of the single nucleotide polymorphism of NOD1 G796A proved to be a high... BeFree 17964870 Detail
0.002 Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site Our results suggest that carriage of the NOD1 G796A mutation increases the susce... BeFree 19882212 Detail
0.014 Inflammatory Bowel Diseases The frequencies of the variant alleles of NOD1 G796A differed significantly betw... BeFree 17964870 Detail
0.001 Helicobacter pylori infection The significance of E266K polymorphism in the NOD1 gene on Helicobacter pylori i... BeFree 19882212 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_006092.4(NOD1):c.796G>A (p.Glu266Lys) AND not provided ClinVar Detail
The aim of this study was to investigate polymorphisms in the NOD2/CARD15 (R702W, G908R, and 3020ins... DisGeNET Detail
The aim of this study was to investigate polymorphisms in the NOD2/CARD15 (R702W, G908R, and 3020ins... DisGeNET Detail
NOD1 gene E266K polymorphism is associated with disease susceptibility but not with disease phenotyp... DisGeNET Detail
Polymorphism in NOD1 G796A alone did not prove to be a risk factor for stroke in general, but in ass... DisGeNET Detail
E266K CARD4/NOD1, but not the TLR4 gene polymorphism increases the risk of peptic ulceration in H. p... DisGeNET Detail
E266K CARD4/NOD1, but not the TLR4 gene polymorphism increases the risk of peptic ulceration in H. p... DisGeNET Detail
NOD1 gene E266K polymorphism is associated with disease susceptibility but not with disease phenotyp... DisGeNET Detail
Carriage of the single nucleotide polymorphism of NOD1 G796A proved to be a highly significant risk ... DisGeNET Detail
Our results suggest that carriage of the NOD1 G796A mutation increases the susceptibility of gastric... DisGeNET Detail
The frequencies of the variant alleles of NOD1 G796A differed significantly between the Crohn's dise... DisGeNET Detail
The significance of E266K polymorphism in the NOD1 gene on Helicobacter pylori infection: an effecti... 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
rs2075820 dbSNP
Genome
hg38
Position
chr7:30,452,621-30,452,621
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1206
Mean of sample read depth (HGVD)
71.09
Standard deviation of sample read depth (HGVD)
35.68
Number of reference allele (HGVD)
1292
Number of alternative allele (HGVD)
1120
Allele Frequency (HGVD)
0.46434494195688225
Gene Symbol (HGVD)
NOD1
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))
rs2075820
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4561
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7643
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
3004
East Asian Heterozygous Counts (ExAC)
1952
East Asian Homozygous Counts (ExAC)
526
East Asian Allele Frequency (ExAC)
0.34954619501978124
Chromosome Counts in All Race (ExAC)
120650
Allele Counts in All Race (ExAC)
33500
Heterozygous Counts in All Race (ExAC)
23620
Homozygous Counts in All Race (ExAC)
4940
Allele Frequency in All Race (ExAC)
0.27766266058847905
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