NM_001370466.1(NOD2):c.616C>T (p.Gln206Ter) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 22, 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:: RCV002553764.10

Allele description [Variation Report for NM_001370466.1(NOD2):c.616C>T (p.Gln206Ter)]

NM_001370466.1(NOD2):c.616C>T (p.Gln206Ter)

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.616C>T (p.Gln206Ter)

HGVS:

NC_000016.10:g.50710608C>T
NG_007508.1:g.18470C>T
NM_001293557.2:c.616C>T
NM_001370466.1:c.616C>TMANE SELECT
NM_022162.3:c.697C>T
NP_001280486.1:p.Gln206Ter
NP_001357395.1:p.Gln206Ter
NP_071445.1:p.Gln233Ter
LRG_177:g.18470C>T
NC_000016.9:g.50744519C>T
NM_022162.2:c.697C>T
NR_163434.1:n.681C>T

Protein change:

Q206*

Links:

dbSNP: rs781333877

NCBI 1000 Genomes Browser:

rs781333877

Molecular consequence:

NR_163434.1:n.681C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_001293557.2:c.616C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001370466.1:c.616C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_022162.3:c.697C>T - nonsense - [Sequence Ontology: SO:0001587]

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
SCV001218200	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 22, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 33692434, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001218200

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 22, 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

Mutation spectrum of NOD2 reveals recessive inheritance as a main driver of Early Onset Crohn's Disease.

Horowitz JE, Warner N, Staples J, Crowley E, Gosalia N, Murchie R, Van Hout C, Fiedler K, Welch G, King AK, Reid JG, Overton JD, Baras A, Shuldiner AR, Griffiths A, Gottesman O, Muise AM, Gonzaga-Jauregui C.

Sci Rep. 2021 Mar 10;11(1):5595. doi: 10.1038/s41598-021-84938-8.

PubMed [citation]

PMID:: 33692434
PMCID:: PMC7946957

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001218200.5

#	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. ClinVar contains an entry for this variant (Variation ID: 849868). This premature translational stop signal has been observed in individual(s) with clinical features of infammatory bowel disease (PMID: 33692434). This variant is present in population databases (rs781333877, gnomAD 0.01%). This sequence change creates a premature translational stop signal (p.Gln233*) in the NOD2 gene. It is expected to result in an absent or disrupted protein product. However, the current clinical and genetic evidence is not sufficient to establish whether loss-of-function variants in NOD2 cause disease.

#	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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