chr16:50710713:C>T Detail (hg38) (NOD2)

Information

Genome

Assembly Position
hg19 chr16:50,744,624-50,744,624 View the variant detail on this assembly version.
hg38 chr16:50,710,713-50,710,713

HGVS

Type Transcript Protein
RefSeq NM_001293557.1:c.802C>T NP_001280486.1:p.Pro268Ser
NM_022162.2:c.802C>T NP_071445.1:p.Pro268Ser
Ensemble ENST00000300589.6:c.802C>T ENST00000300589.6:p.Pro268Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.008

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605956 OMIM
HGNC 5331 HGNC
Ensembl ENSG00000167207 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv55472383 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2017-04-27 criteria provided, single submitter Blau syndrome germline Detail
Benign 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2017-04-27 criteria provided, single submitter inflammatory bowel disease 1 germline Detail
Benign 2023-11-29 criteria provided, single submitter not provided germline Detail
Benign 2022-01-20 criteria provided, single submitter Autoinflammatory syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Regional enteritis,Blau syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Regional enteritis,Blau syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.234 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.327 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.129 ulcerative colitis The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute t... BeFree 22426692 Detail
0.034 Inflammatory Bowel Diseases In all, 612 patients with well-characterised inflammatory bowel disease (252 Sco... BeFree 15190267 Detail
0.002 Inflammatory Bowel Diseases In all, 612 patients with well-characterised inflammatory bowel disease (252 Sco... BeFree 15190267 Detail
0.080 Crohn Disease We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... BeFree 18715515 Detail
0.397 Inflammatory Bowel Diseases In all, 612 patients with well-characterised inflammatory bowel disease (252 Sco... BeFree 15190267 Detail
0.397 Inflammatory Bowel Diseases A case-control study of NOD2 polymorphisms known to be associated with Crohn's d... BeFree 12115195 Detail
0.234 ulcerative colitis A case-control study of NOD2 polymorphisms known to be associated with Crohn's d... BeFree 12115195 Detail
0.012 Inflammatory Bowel Diseases In all, 612 patients with well-characterised inflammatory bowel disease (252 Sco... BeFree 15190267 Detail
0.560 Crohn Disease We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... BeFree 18715515 Detail
0.080 Crohn Disease We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... BeFree 18715515 Detail
0.368 Crohn Disease We confirmed a strong association between three NOD2/CARD15 gene variants (Pro26... BeFree 18715515 Detail
0.234 ulcerative colitis Recent studies from India have reported an association with UC and a single poly... BeFree 24145928 Detail
0.560 Crohn Disease A case-control study of NOD2 polymorphisms known to be associated with Crohn's d... BeFree 12115195 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND Blau syndrome ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND not specified ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND Inflammatory bowel disease 1 ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND not provided ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND Autoinflammatory syndrome ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND multiple conditions ClinVar Detail
NM_001370466.1(NOD2):c.721C>T (p.Pro241Ser) AND multiple conditions ClinVar Detail
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
The study indicates that IL23R-rs11805303 and PTPN2-rs2542151 might contribute to the development of... DisGeNET Detail
In all, 612 patients with well-characterised inflammatory bowel disease (252 Scottish CD, 247 Scotti... DisGeNET Detail
In all, 612 patients with well-characterised inflammatory bowel disease (252 Scottish CD, 247 Scotti... DisGeNET Detail
We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... DisGeNET Detail
In all, 612 patients with well-characterised inflammatory bowel disease (252 Scottish CD, 247 Scotti... DisGeNET Detail
A case-control study of NOD2 polymorphisms known to be associated with Crohn's disease (CD) (Pro(268... DisGeNET Detail
A case-control study of NOD2 polymorphisms known to be associated with Crohn's disease (CD) (Pro(268... DisGeNET Detail
In all, 612 patients with well-characterised inflammatory bowel disease (252 Scottish CD, 247 Scotti... DisGeNET Detail
We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... DisGeNET Detail
We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... DisGeNET Detail
We confirmed a strong association between three NOD2/CARD15 gene variants (Pro268Ser, OR = 2.52, 95%... DisGeNET Detail
Recent studies from India have reported an association with UC and a single polymorphism (SNP) in CA... DisGeNET Detail
A case-control study of NOD2 polymorphisms known to be associated with Crohn's disease (CD) (Pro(268... 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
rs2066842 dbSNP
Genome
hg38
Position
chr16:50,710,713-50,710,713
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1204
Mean of sample read depth (HGVD)
40.13
Standard deviation of sample read depth (HGVD)
19.12
Number of reference allele (HGVD)
2405
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0012458471760797341
Gene Symbol (HGVD)
NOD2
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))
rs2066842
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8564
East Asian Allele Counts (ExAC)
68
East Asian Heterozygous Counts (ExAC)
68
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.007940214852872489
Chromosome Counts in All Race (ExAC)
119820
Allele Counts in All Race (ExAC)
22098
Heterozygous Counts in All Race (ExAC)
17058
Homozygous Counts in All Race (ExAC)
2520
Allele Frequency in All Race (ExAC)
0.1844266399599399
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