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NM_001370466.1(NOD2):c.2886G>A (p.Lys962=) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 22, 2020
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:
RCV002547036.9

Allele description

NM_001370466.1(NOD2):c.2886G>A (p.Lys962=)

Genes:
CYLD-AS1:CYLD antisense RNA 1 [Gene - HGNC]
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.2886G>A (p.Lys962=)
HGVS:
  • NC_000016.10:g.50729818G>A
  • NG_007508.1:g.37680G>A
  • NM_001293557.2:c.2886G>A
  • NM_001370466.1:c.2886G>AMANE SELECT
  • NM_022162.3:c.2967G>A
  • NP_001280486.1:p.Lys962=
  • NP_001357395.1:p.Lys962=
  • NP_071445.1:p.Lys989=
  • LRG_177:g.37680G>A
  • NC_000016.9:g.50763729G>A
  • NR_163434.1:n.3098G>A
Links:
dbSNP: rs1965389837
NCBI 1000 Genomes Browser:
rs1965389837
Molecular consequence:
  • NR_163434.1:n.3098G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001293557.2:c.2886G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370466.1:c.2886G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_022162.3:c.2967G>A - synonymous variant - [Sequence Ontology: SO:0001819]

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001539671Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 22, 2020) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

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 Invitae, SCV001539671.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant is not likely to affect RNA splicing, but this prediction has not been confirmed by published transcriptional studies. This variant has not been reported in the literature in individuals with NOD2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change affects codon 989 of the NOD2 mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NOD2 protein.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 16, 2024