NM_001370466.1(NOD2):c.2585A>C (p.Gln862Pro) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 23, 2023
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:: RCV003803785.1

Allele description [Variation Report for NM_001370466.1(NOD2):c.2585A>C (p.Gln862Pro)]

NM_001370466.1(NOD2):c.2585A>C (p.Gln862Pro)

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.2585A>C (p.Gln862Pro)

HGVS:

NC_000016.10:g.50719960A>C
NG_007508.1:g.27822A>C
NM_001293557.2:c.2585A>C
NM_001370466.1:c.2585A>CMANE SELECT
NM_022162.3:c.2666A>C
NP_001280486.1:p.Gln862Pro
NP_001357395.1:p.Gln862Pro
NP_071445.1:p.Gln889Pro
NP_071445.1:p.Gln889Pro
LRG_177t1:c.2666A>C
LRG_177:g.27822A>C
LRG_177p1:p.Gln889Pro
NC_000016.9:g.50753871A>C
NM_022162.1:c.2666A>C
NR_163434.1:n.2797A>C

Protein change:

Q862P

Molecular consequence:

NM_001293557.2:c.2585A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001370466.1:c.2585A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_022162.3:c.2666A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_163434.1:n.2797A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Blau syndrome (BLAUS)
Synonyms:: Synovitis granulomatous with uveitis and cranial neuropathies; Arthrocutaneouveal granulomatosis; Granulomatosis, familial, Blau type; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008523; MedGen: C5201146; Orphanet: 90340; OMIM: 186580

Name:: Regional enteritis
Synonyms:: Enteritis, Granulomatous
Identifiers:: MeSH: D003424; MedGen: C0678202

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004594016	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Mar 23, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 15044951, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004594016

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Mar 23, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Regulatory regions and critical residues of NOD2 involved in muramyl dipeptide recognition.

Tanabe T, Chamaillard M, Ogura Y, Zhu L, Qiu S, Masumoto J, Ghosh P, Moran A, Predergast MM, Tromp G, Williams CJ, Inohara N, Núñez G.

EMBO J. 2004 Apr 7;23(7):1587-97. Epub 2004 Mar 25.

PubMed [citation]

PMID:: 15044951
PMCID:: PMC391079

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV004594016.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Experimental studies have shown that this missense change does not substantially affect NOD2 function (PMID: 15044951). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt NOD2 protein function. This variant has not been reported in the literature in individuals affected with NOD2-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces glutamine, which is neutral and polar, with proline, which is neutral and non-polar, at codon 889 of the NOD2 protein (p.Gln889Pro).

#	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: Mar 5, 2024

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