NM_001370466.1(NOD2):c.667G>A (p.Asp223Asn) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 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:: RCV002609233.3

Allele description [Variation Report for NM_001370466.1(NOD2):c.667G>A (p.Asp223Asn)]

NM_001370466.1(NOD2):c.667G>A (p.Asp223Asn)

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.667G>A (p.Asp223Asn)

HGVS:

NC_000016.10:g.50710659G>A
NG_007508.1:g.18521G>A
NM_001293557.2:c.667G>A
NM_001370466.1:c.667G>AMANE SELECT
NM_022162.3:c.748G>A
NP_001280486.1:p.Asp223Asn
NP_001357395.1:p.Asp223Asn
NP_071445.1:p.Asp250Asn
NP_071445.1:p.Asp250Asn
LRG_177t1:c.748G>A
LRG_177:g.18521G>A
LRG_177p1:p.Asp250Asn
NC_000016.9:g.50744570G>A
NM_022162.1:c.748G>A
NR_163434.1:n.732G>A

Protein change:

D223N

Molecular consequence:

NM_001293557.2:c.667G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370466.1:c.667G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_022162.3:c.748G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_163434.1:n.732G>A - 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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RecName: Full=PRAME family member 9
RecName: Full=PRAME family member 9
gi|2152672145|sp|P0DUQ2.1|PRAM9_HUM

Protein
NXPH4 neurexophilin 4 [Homo sapiens]
NXPH4 neurexophilin 4 [Homo sapiens]
Gene ID:11247

Gene
Snapc5 small nuclear RNA activating complex, polypeptide 5 [Mus musculus]
Snapc5 small nuclear RNA activating complex, polypeptide 5 [Mus musculus]
Gene ID:330959

Gene
330959[uid] AND (alive[prop]) (1)
Gene
nssv1945207 (1)
dbVar

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002968080	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 22, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002968080

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 22, 2023)

germline

clinical testing

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

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

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, SCV002968080.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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. 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. ClinVar contains an entry for this variant (Variation ID: 1923914). 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 aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 250 of the NOD2 protein (p.Asp250Asn).

#	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: Sep 29, 2024

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