NM_001243133.2(NLRP3):c.1639A>T (p.Ser547Cys) AND not provided

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Oct 7, 2021)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_001243133.2(NLRP3):c.1639A>T (p.Ser547Cys)]

NM_001243133.2(NLRP3):c.1639A>T (p.Ser547Cys)

NLRP3:NLR family pyrin domain containing 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001243133.2(NLRP3):c.1639A>T (p.Ser547Cys)
  • NC_000001.11:g.247425088A>T
  • NG_007509.2:g.13916A>T
  • NM_001079821.2:c.1645A>T
  • NM_001079821.3:c.1639A>T
  • NM_001127461.3:c.1639A>T
  • NM_001127462.3:c.1639A>T
  • NM_001243133.2:c.1639A>TMANE SELECT
  • NM_004895.4:c.1645A>T
  • NM_004895.5:c.1645A>T
  • NM_183395.3:c.1639A>T
  • NP_001073289.1:p.Ser549Cys
  • NP_001073289.2:p.Ser547Cys
  • NP_001120933.2:p.Ser547Cys
  • NP_001120934.2:p.Ser547Cys
  • NP_001230062.1:p.Ser547Cys
  • NP_004886.3:p.Ser549Cys
  • NP_004886.3:p.Ser549Cys
  • NP_899632.2:p.Ser547Cys
  • LRG_197t1:c.1645A>T
  • LRG_197:g.13916A>T
  • LRG_197p1:p.Ser549Cys
  • NC_000001.10:g.247588390A>T
  • p.Ser549Cys
Protein change:
dbSNP: rs139833874
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001079821.2:c.1645A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001079821.3:c.1639A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127461.3:c.1639A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127462.3:c.1639A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001243133.2:c.1639A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004895.4:c.1645A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004895.5:c.1645A>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_183395.3:c.1639A>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001144769Athena Diagnostics Inccriteria provided, single submitter
(Mar 21, 2019)
germlineclinical testing

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

SCV001767111GeneDxcriteria provided, single submitter
Uncertain significance
(Oct 7, 2021)
germlineclinical testing

Citation Link

Summary from all submissions

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



A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

Details of each submission

From Athena Diagnostics Inc, SCV001144769.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From GeneDx, SCV001767111.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


Observed in two patients with NLRP3-related disorders in the published literature (Lane et al., 2015; Brighouse et al., 2018); In silico analysis supports that this missense variant does not alter protein structure/function; Also known as p.S547C

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 6, 2021

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