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NM_144687.4(NLRP12):c.1952C>A (p.Ser651Ter) AND Familial cold autoinflammatory syndrome 2

Germline classification:
Conflicting classifications of pathogenicity (2 submissions)
Last evaluated:
Dec 16, 2020
Review status:
criteria provided, conflicting classifications
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:
RCV001269323.14

Allele description [Variation Report for NM_144687.4(NLRP12):c.1952C>A (p.Ser651Ter)]

NM_144687.4(NLRP12):c.1952C>A (p.Ser651Ter)

Gene:
NLRP12:NLR family pyrin domain containing 12 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19q13.42
Genomic location:
Preferred name:
NM_144687.4(NLRP12):c.1952C>A (p.Ser651Ter)
HGVS:
  • NC_000019.10:g.53809707G>T
  • NG_008651.2:g.19688C>A
  • NM_001277126.2:c.1952C>A
  • NM_001277129.1:c.1952C>A
  • NM_144687.4:c.1952C>AMANE SELECT
  • NP_001264055.1:p.Ser651Ter
  • NP_001264058.1:p.Ser651Ter
  • NP_653288.1:p.Ser651Ter
  • LRG_181t1:c.1952C>A
  • LRG_181t2:c.1952C>A
  • LRG_181:g.19688C>A
  • LRG_181p1:p.Ser651Ter
  • LRG_181p2:p.Ser651Ter
  • NC_000019.9:g.54312961G>T
  • NG_008651.1:g.19688C>A
  • NM_144687.3:c.1952C>A
Protein change:
S651*
Links:
dbSNP: rs781361326
Molecular consequence:
  • NM_001277126.2:c.1952C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001277129.1:c.1952C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_144687.4:c.1952C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Familial cold autoinflammatory syndrome 2 (FCAS2)
Identifiers:
MONDO: MONDO:0012724; MedGen: C2673198; Orphanet: 247868; OMIM: 611762

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001448259Dubai Health Genomic Medicine Center, Dubai Health
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Oct 4, 2020)
germlineclinical testing

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

SCV002050258ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process 2021)
Uncertain significance
(Dec 16, 2020)
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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Dubai Health Genomic Medicine Center, Dubai Health, SCV001448259.2

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002050258.1

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

Description

The NLRP12 c.1952C>A; p.Ser651Ter variant (rs781361326), to our knowledge, is not reported in the medical literature or gene-specific databases. This variant is found on only four chromosomes (4/251382 alleles) in the Genome Aggregation Database. This variant induces an early termination codon and is predicted to result in a truncated protein or mRNA subject to nonsense-mediated decay. While loss-of-function variants in NLRP12 have been reported in individuals affected with autoinflammatory disease or periodic fever syndromes (Hua 2019, Jeru 2008, Kostik 2018, Xia 2016), the mechanism by which such variants cause disease remains uncertain (Tuncer 2014). Due to limited information, the clinical significance of the p.Ser651Ter variant is uncertain at this time. References: Hua Y et al. Phenotypes and genotypes of Chinese adult patients with systemic autoinflammatory diseases. Semin Arthritis Rheum. 2019 Dec;49(3):446-452. Jeru I et al. Mutations in NALP12 cause hereditary periodic fever syndromes. Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1614-9. Kostik MM et al. Multigene sequencing reveals heterogeneity of NLRP12-related autoinflammatory disorders. Rheumatol Int. 2018 May;38(5):887-893. Tuncer S et al. The multifaceted nature of NLRP12. J Leukoc Biol. 2014 Dec;96(6):991-1000. Xia X et al. Identification of a Novel NLRP12 Nonsense Mutation (Trp408X) in the Extremely Rare Disease FCAS by Exome Sequencing. PLoS One. 2016 Jun 17;11(6):e0156981.

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

Last Updated: Dec 1, 2025

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