NM_001370466.1(NOD2):c.1969C>T (p.Arg657Trp) AND Inflammatory bowel disease 1

Germline classification:: Likely benign (1 submission)
Last evaluated:: Apr 28, 2017
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001782820.12

Allele description [Variation Report for NM_001370466.1(NOD2):c.1969C>T (p.Arg657Trp)]

NM_001370466.1(NOD2):c.1969C>T (p.Arg657Trp)

Gene:

NOD2:nucleotide binding oligomerization domain containing 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_001370466.1(NOD2):c.1969C>T (p.Arg657Trp)

HGVS:

NC_000016.10:g.50711961C>T
NG_007508.1:g.19823C>T
NM_001293557.2:c.1969C>T
NM_001370466.1:c.1969C>TMANE SELECT
NM_022162.3:c.2050C>T
NP_001280486.1:p.Arg657Trp
NP_001357395.1:p.Arg657Trp
NP_071445.1:p.Arg684Trp
LRG_177t1:c.2050C>T
LRG_177:g.19823C>T
NC_000016.9:g.50745872C>T
NM_022162.1:c.2050C>T
NM_022162.2:c.2050C>T
NR_163434.1:n.2034C>T
Q9HC29:p.Arg684Trp

Protein change:

R657W

Links:

UniProtKB: Q9HC29#VAR_012688; dbSNP: rs5743276

NCBI 1000 Genomes Browser:

rs5743276

Molecular consequence:

NM_001293557.2:c.1969C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001370466.1:c.1969C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_022162.3:c.2050C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_163434.1:n.2034C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Inflammatory bowel disease 1 (IBD1)
Synonyms:: Inflammatory bowel disease 1, Crohn disease; INFLAMMATORY BOWEL DISEASE (CROHN DISEASE) 1
Identifiers:: MONDO: MONDO:0009960; MedGen: CN260071; OMIM: 266600

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000397253	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Apr 28, 2017)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 26316104, 12626759, 11875755, 20032092 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000397253

Illumina Laboratory Services, Illumina

criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)

Likely benign
(Apr 28, 2017)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Variations in inflammatory genes as molecular markers for prediction of inflammatory bowel disease occurrence.

Stankovic B, Dragasevic S, Popovic D, Zukic B, Kotur N, Sokic-Milutinovic A, Alempijevic T, Lukic S, Milosavljevic T, Nikcevic G, Pavlovic S.

J Dig Dis. 2015 Dec;16(12):723-33. doi: 10.1111/1751-2980.12281.

PubMed [citation]

PMID:: 26316104

Gene-environment interaction modulated by allelic heterogeneity in inflammatory diseases.

Chamaillard M, Philpott D, Girardin SE, Zouali H, Lesage S, Chareyre F, Bui TH, Giovannini M, Zaehringer U, Penard-Lacronique V, Sansonetti PJ, Hugot JP, Thomas G.

Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3455-60. Epub 2003 Mar 7.

PubMed [citation]

PMID:: 12626759
PMCID:: PMC152314

See all PubMed Citations (4)

Details of each submission

From Illumina Laboratory Services, Illumina, SCV000397253.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

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, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 10, 2024

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