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NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(4);Uncertain significance(2)

Review status:
criteria provided, conflicting interpretations
Submissions:
6 (Most recent: Jul 4, 2021)
Last evaluated:
Nov 25, 2020
Accession:
VCV000197333.14
Variation ID:
197333
Description:
single nucleotide variant
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NM_001370466.1(NOD2):c.2026C>T (p.Arg676Cys)

Allele ID
194494
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q12.1
Genomic location
16: 50712018 (GRCh38) GRCh38 UCSC
16: 50745929 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
Q9HC29:p.Arg703Cys
NC_000016.10:g.50712018C>T
NC_000016.9:g.50745929C>T
... more HGVS
Protein change
R703C, R676C
Other names
-
Canonical SPDI
NC_000016.10:50712017:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
0.00100 (T)

Allele frequency
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00500
The Genome Aggregation Database (gnomAD) 0.00283
1000 Genomes Project 0.00100
Trans-Omics for Precision Medicine (TOPMed) 0.00426
Links
ClinGen: CA202825
UniProtKB: Q9HC29#VAR_012690
dbSNP: rs5743277
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Oct 24, 2014 RCV000178334.1
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000330236.2
Likely benign 1 criteria provided, single submitter Apr 27, 2017 RCV000368536.2
Uncertain significance 1 criteria provided, single submitter Sep 1, 2016 RCV000488013.5
Likely benign 1 criteria provided, single submitter Nov 25, 2020 RCV001086759.2
Uncertain significance 1 criteria provided, single submitter Dec 17, 2019 RCV001289749.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NOD2 - - GRCh38
GRCh37
536 561

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Oct 24, 2014)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230397.5
Submitted: (Sep 19, 2018)
Evidence details
Publications
PubMed (4)
Other databases
http://www.egl-eurofins.com/emvc…
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Inflammatory bowel disease 1
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000397256.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (8)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Likely benign
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Blau syndrome
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV000397257.3
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (2)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Dec 17, 2019)
criteria provided, single submitter
Method: clinical testing
none provided
Allele origin: germline
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001477731.1
Submitted: (Dec 11, 2020)
Evidence details
Comment:
The NOD2 c.2107C>; p.Arg703Cys (rs5743277) variant has been described in the literature in individuals with autoinflammatory disease (Shen 2015, Yao 2012). The variant has also … (more)
Likely benign
(Nov 25, 2020)
criteria provided, single submitter
Method: clinical testing
Inflammatory bowel disease 1
Blau syndrome
Allele origin: germline
Invitae
Accession: SCV000759547.4
Submitted: (Jan 07, 2021)
Evidence details
Uncertain significance
(Sep 01, 2016)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000575052.12
Submitted: (Jul 04, 2021)
Evidence details

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Granulomatous disease associated with NOD2 sequence variants and familial camptodactyly: An intermediate form of NOD2-associated diseases? Shen M Seminars in arthritis and rheumatism 2015 PMID: 26164256
Prediction of Crohn's disease aggression through NOD2/CARD15 gene sequencing in an Australian cohort. Bhullar M World journal of gastroenterology 2014 PMID: 24803813
Granulomatous pneumonitis associated with adult-onset Blau-like syndrome. Yao Q American journal of respiratory and critical care medicine 2012 PMID: 22942351
Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Rivas MA Nature genetics 2011 PMID: 21983784
Mutation, selection, and evolution of the Crohn disease susceptibility gene CARD15. King K Human mutation 2006 PMID: 16278823
Toll-like receptor 4 and NOD2/CARD15 mutations in Hungarian patients with Crohn's disease: phenotype-genotype correlations. Lakatos PL World journal of gastroenterology 2005 PMID: 15770725
[NOD2/CARD15 mutations and genotype-phenotype correlations in patients with Crohn's disease. Hungarian multicenter study]. Lakatos L Orvosi hetilap 2004 PMID: 15320482
Crohn disease: frequency and nature of CARD15 mutations in Ashkenazi and Sephardi/Oriental Jewish families. Tukel T American journal of human genetics 2004 PMID: 15024686
Gene-environment interaction modulated by allelic heterogeneity in inflammatory diseases. Chamaillard M Proceedings of the National Academy of Sciences of the United States of America 2003 PMID: 12626759
CARD15/NOD2 mutational analysis and genotype-phenotype correlation in 612 patients with inflammatory bowel disease. Lesage S American journal of human genetics 2002 PMID: 11875755
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=NOD2 - - - -

Text-mined citations for rs5743277...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 11, 2021