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NM_001243133.2(NLRP3):c.1365C>A (p.Ser455Arg) AND Cryopyrin associated periodic syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 19, 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:
RCV001943527.4

Allele description [Variation Report for NM_001243133.2(NLRP3):c.1365C>A (p.Ser455Arg)]

NM_001243133.2(NLRP3):c.1365C>A (p.Ser455Arg)

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.1365C>A (p.Ser455Arg)
HGVS:
  • NC_000001.11:g.247424814C>A
  • NG_007509.2:g.13642C>A
  • NM_001079821.3:c.1365C>A
  • NM_001127461.3:c.1365C>A
  • NM_001127462.3:c.1365C>A
  • NM_001243133.2:c.1365C>AMANE SELECT
  • NM_004895.5:c.1371C>A
  • NM_183395.3:c.1365C>A
  • NP_001073289.2:p.Ser455Arg
  • NP_001120933.2:p.Ser455Arg
  • NP_001120934.2:p.Ser455Arg
  • NP_001230062.1:p.Ser455Arg
  • NP_004886.3:p.Ser457Arg
  • NP_899632.2:p.Ser455Arg
  • LRG_197:g.13642C>A
  • NC_000001.10:g.247588116C>A
Protein change:
S455R
Links:
dbSNP: rs777985232
NCBI 1000 Genomes Browser:
rs777985232
Molecular consequence:
  • NM_001079821.3:c.1365C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127461.3:c.1365C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127462.3:c.1365C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243133.2:c.1365C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004895.5:c.1371C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_183395.3:c.1365C>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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002189583Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Sep 19, 2022) 		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 Labcorp Genetics (formerly Invitae), Labcorp, SCV002189583.3

#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. 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 NLRP3 protein function. ClinVar contains an entry for this variant (Variation ID: 1420378). This variant has not been reported in the literature in individuals affected with NLRP3-related conditions. This variant is present in population databases (rs777985232, gnomAD 0.003%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 457 of the NLRP3 protein (p.Ser457Arg).

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

Last Updated: Sep 29, 2024