NM_001243133.2(NLRP3):c.2098G>A (p.Asp700Asn) AND Cryopyrin associated periodic syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 4, 2022
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:: RCV001855717.3

Allele description [Variation Report for NM_001243133.2(NLRP3):c.2098G>A (p.Asp700Asn)]

NM_001243133.2(NLRP3):c.2098G>A (p.Asp700Asn)

Gene:

NLRP3:NLR family pyrin domain containing 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q44

Genomic location:

Preferred name:

NM_001243133.2(NLRP3):c.2098G>A (p.Asp700Asn)

HGVS:

NC_000001.11:g.247425547G>A
NG_007509.2:g.14375G>A
NM_001079821.3:c.2098G>A
NM_001127461.3:c.2098G>A
NM_001127462.3:c.2098G>A
NM_001243133.2:c.2098G>AMANE SELECT
NM_004895.5:c.2104G>A
NM_183395.3:c.2098G>A
NP_001073289.2:p.Asp700Asn
NP_001120933.2:p.Asp700Asn
NP_001120934.2:p.Asp700Asn
NP_001230062.1:p.Asp700Asn
NP_004886.3:p.Asp702Asn
NP_004886.3:p.Asp702Asn
NP_899632.2:p.Asp700Asn
LRG_197t1:c.2104G>A
LRG_197:g.14375G>A
LRG_197p1:p.Asp702Asn
NC_000001.10:g.247588849G>A
NM_004895.4:c.2104G>A

Protein change:

D700N

Links:

dbSNP: rs781561828

NCBI 1000 Genomes Browser:

rs781561828

Molecular consequence:

NM_001079821.3:c.2098G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127461.3:c.2098G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127462.3:c.2098G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243133.2:c.2098G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004895.5:c.2104G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_183395.3:c.2098G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cryopyrin associated periodic syndrome (CAPS)
Identifiers:: MONDO: MONDO:0016168; MedGen: C2316212

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002259016	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 4, 2022)	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

SCV002259016

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 4, 2022)

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, SCV002259016.2

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

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 702 of the NLRP3 protein (p.Asp702Asn). This variant is present in population databases (rs781561828, gnomAD 0.04%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with NLRP3-related conditions. ClinVar contains an entry for this variant (Variation ID: 625986). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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.

#	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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