NM_001243133.2(NLRP3):c.1467T>A (p.Asn489Lys) AND Cryopyrin associated periodic syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 8, 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:: RCV001948139.6

Allele description [Variation Report for NM_001243133.2(NLRP3):c.1467T>A (p.Asn489Lys)]

NM_001243133.2(NLRP3):c.1467T>A (p.Asn489Lys)

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.1467T>A (p.Asn489Lys)

HGVS:

NC_000001.11:g.247424916T>A
NG_007509.2:g.13744T>A
NM_001079821.3:c.1467T>A
NM_001127461.3:c.1467T>A
NM_001127462.3:c.1467T>A
NM_001243133.2:c.1467T>AMANE SELECT
NM_004895.5:c.1473T>A
NM_183395.3:c.1467T>A
NP_001073289.2:p.Asn489Lys
NP_001120933.2:p.Asn489Lys
NP_001120934.2:p.Asn489Lys
NP_001230062.1:p.Asn489Lys
NP_004886.3:p.Asn491Lys
NP_899632.2:p.Asn489Lys
LRG_197:g.13744T>A
NC_000001.10:g.247588218T>A

Protein change:

N489K

Links:

dbSNP: rs2103110971

NCBI 1000 Genomes Browser:

rs2103110971

Molecular consequence:

NM_001079821.3:c.1467T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127461.3:c.1467T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001127462.3:c.1467T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001243133.2:c.1467T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_004895.5:c.1473T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_183395.3:c.1467T>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
SCV002188555	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 8, 2020)	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

SCV002188555

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 8, 2020)

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, SCV002188555.3

#	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. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The lysine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with NLRP3-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces asparagine with lysine at codon 491 of the NLRP3 protein (p.Asn491Lys). The asparagine residue is moderately conserved and there is a moderate physicochemical difference between asparagine and lysine.

#	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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