ClinVar Genomic variation as it relates to human health
NM_001243133.2(NLRP3):c.1316C>T (p.Ala439Val)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001243133.2(NLRP3):c.1316C>T (p.Ala439Val)
Variation ID: 4370 Accession: VCV000004370.28
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 1q44 1: 247424765 (GRCh38) [ NCBI UCSC ] 1: 247588067 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 6, 2014 Feb 14, 2024 Sep 20, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001243133.2:c.1316C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001230062.1:p.Ala439Val missense NM_001079821.3:c.1316C>T NP_001073289.2:p.Ala439Val missense NM_001127461.3:c.1316C>T NP_001120933.2:p.Ala439Val missense NM_001127462.3:c.1316C>T NP_001120934.2:p.Ala439Val missense NM_004895.5:c.1322C>T NP_004886.3:p.Ala441Val missense NM_183395.3:c.1316C>T NP_899632.2:p.Ala439Val missense NC_000001.11:g.247424765C>T NC_000001.10:g.247588067C>T NG_007509.2:g.13593C>T LRG_197:g.13593C>T LRG_197t1:c.1322C>T LRG_197p1:p.Ala441Val - Protein change
- A439V, A441V
- Other names
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- Canonical SPDI
- NC_000001.11:247424764:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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NLRP3 | - | - |
GRCh38 GRCh38 GRCh37 |
980 | 1063 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Likely pathogenic (3) |
criteria provided, single submitter
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Jul 26, 2023 | RCV000004618.17 | |
Pathogenic (4) |
criteria provided, multiple submitters, no conflicts
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Nov 23, 2022 | RCV000214900.23 | |
Pathogenic (1) |
criteria provided, single submitter
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Sep 20, 2023 | RCV000701554.16 | |
Pathogenic (1) |
criteria provided, single submitter
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Jul 29, 2021 | RCV002476928.8 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 6, 2021 | RCV002262553.10 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Pathogenic
(Jan 06, 2021)
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criteria provided, single submitter
Method: clinical testing
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Autoinflammatory syndrome
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002542594.1
First in ClinVar: Jul 09, 2022 Last updated: Jul 09, 2022 |
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Pathogenic
(Jul 29, 2021)
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criteria provided, single submitter
Method: clinical testing
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Familial cold autoinflammatory syndrome 1
Keratitis fugax hereditaria Familial amyloid nephropathy with urticaria AND deafness Chronic infantile neurological, cutaneous and articular syndrome Hearing loss, autosomal dominant 34, with or without inflammation
Affected status: unknown
Allele origin:
unknown
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Fulgent Genetics, Fulgent Genetics
Accession: SCV002784124.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
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Pathogenic
(Nov 23, 2022)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000885859.5
First in ClinVar: Dec 19, 2017 Last updated: Mar 04, 2023 |
Comment:
The NLRP3 c.1322C>T; p.Ala441Val variant (rs121908146), also known as Ala439Val, is published in the medical literature in several individuals and families with various autoinflammatory syndromes … (more)
The NLRP3 c.1322C>T; p.Ala441Val variant (rs121908146), also known as Ala439Val, is published in the medical literature in several individuals and families with various autoinflammatory syndromes (Aoyama 2012, Hentgen 2005, Hoffman 2001, Houx 2015, Parker 2016) and is described as one of the more common pathogenic variants (Cuisset 2010). The variant is described as occurring de novo in at least one family (Hoffman 2001) and also has been shown to segregate with disease (Hoffman 2001, Hentgen 2005). The variant is reported in ClinVar (Variation ID: 4370), but is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. The alanine at codon 441 is highly conserved, and computational analyses are uncertain whether this variant is neutral or deleterious (REVEL: 0.481). Considering available information, this variant is classified as pathogenic. References: Aoyama K et al. Cryopyrin-associated periodic syndrome: a case report and review of the Japanese literature. Acta Derm Venereol. 2012 Jul;92(4):395-8. PMID: 22377911. Cuisset L et al. Mutations in the autoinflammatory cryopyrin-associated periodic syndrome gene: epidemiological study and lessons from eight years of genetic analysis in France. Ann Rheum Dis. 2011 Mar;70(3):495-9. PMID: 21109514. Hentgen V et al. Intrafamilial variable phenotypic expression of a CIAS1 mutation: from Muckle-Wells to chronic infantile neurological cutaneous and articular syndrome. J Rheumatol. 2005 Apr;32(4):747-51. PMID: 15801036. PMID: 11687797. Hoffman HM et al. Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. Nat Genet. 2001 Nov;29(3):301-5. PMID: 11687797. Houx L et al. Musculoskeletal symptoms in patients with cryopyrin-associated periodic syndromes: a large database study. Arthritis Rheumatol. 2015 Nov;67(11):3027-36. PMID: 26245507. Parker T et al. Neurology of the cryopyrin-associated periodic fever syndrome. Eur J Neurol. 2016 Jul;23(7):1145-51. PMID: 26931528. (less)
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Likely pathogenic
(Jul 26, 2023)
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criteria provided, single submitter
Method: clinical testing
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Familial cold autoinflammatory syndrome 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Genetics and Molecular Pathology, SA Pathology
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002761654.2
First in ClinVar: Dec 17, 2022 Last updated: Dec 17, 2023 |
Comment:
The NLRP3 c.1316C>T variant is classified as Likely Pathogenic (PS4_Moderate, PM2, PP1_Strong) The NLRP3 c.1316C>T variant (also known as p.Ala441Val) is a single nucleotide change … (more)
The NLRP3 c.1316C>T variant is classified as Likely Pathogenic (PS4_Moderate, PM2, PP1_Strong) The NLRP3 c.1316C>T variant (also known as p.Ala441Val) is a single nucleotide change in exon 3/9 of the NLRP3 gene, which is predicted to change the amino acid alanine at position 439 in the protein to valine. The variant has been reported in probands with a clinical presentation of Familial Cold Autoinflammatory Syndrome (PS4_Moderate). This variant is absent from population databases (PM2). Segregation with disease is noted within 2 large families, with 19 mutation positive individuals. (PP1_strong) (PubMed: 11687797, 27134254). The variant has been reported in dbSNP (rs121908146) and in the HGMD database: CM013248. It has been reported as Pathogenic by other diagnostic laboratories (ClinVar Variation ID: 4370). (less)
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Pathogenic
(Jun 01, 2021)
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criteria provided, single submitter
Method: clinical testing
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Not Provided
Affected status: yes
Allele origin:
germline
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GeneDx
Accession: SCV000278944.6
First in ClinVar: May 29, 2016 Last updated: Dec 19, 2017 |
Comment:
Published functional studies demonstrate that individuals with A441V have increased secretion of inflammatory cytokines, which correlates with disease severity (Rieber et al., 2015); Not observed … (more)
Published functional studies demonstrate that individuals with A441V have increased secretion of inflammatory cytokines, which correlates with disease severity (Rieber et al., 2015); Not observed at significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26115477, 22377911, 25596455, 26245507, 11687797, 26931528, 27134254, 28956000, 15801036, 31057541, 30568124, 31777803, 27535533, 19302049) (less)
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Pathogenic
(Sep 20, 2023)
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criteria provided, single submitter
Method: clinical testing
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Cryopyrin associated periodic syndrome
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000830359.7
First in ClinVar: Oct 10, 2018 Last updated: Feb 14, 2024 |
Comment:
For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, … (more)
For these reasons, this variant has been classified as Pathogenic. 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on NLRP3 protein function. ClinVar contains an entry for this variant (Variation ID: 4370). This variant is also known as A439V or C1316T. This missense change has been observed in individuals with NLRP3-related disease (PMID: 11687797, 15801036, 25596455, 26245507, 26931528, 27134254). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 441 of the NLRP3 protein (p.Ala441Val). (less)
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Pathogenic
(Nov 01, 2001)
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no assertion criteria provided
Method: literature only
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FAMILIAL COLD AUTOINFLAMMATORY SYNDROME 1
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000024792.3
First in ClinVar: Apr 04, 2013 Last updated: Sep 18, 2016 |
Comment on evidence:
In a 4-generation family with familial cold autoinflammatory syndrome (FCAS1; 120100) previously reported by Shepard (1971), Hoffman et al. (2001) identified a C-to-T transition at … (more)
In a 4-generation family with familial cold autoinflammatory syndrome (FCAS1; 120100) previously reported by Shepard (1971), Hoffman et al. (2001) identified a C-to-T transition at nucleotide 1316 in exon 3 of the CIAS1 gene, resulting in an alanine-to-valine substitution at codon 439 (A439V). (less)
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001958584.1 First in ClinVar: Oct 02, 2021 Last updated: Oct 02, 2021 |
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Pathogenic
(-)
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no assertion criteria provided
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
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Genome Diagnostics Laboratory, University Medical Center Utrecht
Additional submitter:
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Study: VKGL Data-share Consensus
Accession: SCV001931798.1 First in ClinVar: Sep 26, 2021 Last updated: Sep 26, 2021 |
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not provided
(-)
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no classification provided
Method: not provided
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Familial cold urticaria
Affected status: not provided
Allele origin:
unknown
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Unité médicale des maladies autoinflammatoires, CHRU Montpellier
Accession: SCV000116318.1
First in ClinVar: Mar 06, 2014 Last updated: Mar 06, 2014
Comment:
also involved in OMIM 191900 and 607115
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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NLRP3 A439V Mutation in a Large Family with Cryopyrin-associated Periodic Syndrome: Description of Ophthalmologic Symptoms in Correlation with Other Organ Symptoms. | Sobolewska B | The Journal of rheumatology | 2016 | PMID: 27134254 |
Neurology of the cryopyrin-associated periodic fever syndrome. | Parker T | European journal of neurology | 2016 | PMID: 26931528 |
Musculoskeletal symptoms in patients with cryopyrin-associated periodic syndromes: a large database study. | Houx L | Arthritis & rheumatology (Hoboken, N.J.) | 2015 | PMID: 26245507 |
A functional inflammasome activation assay differentiates patients with pathogenic NLRP3 mutations and symptomatic patients with low penetrance variants. | Rieber N | Clinical immunology (Orlando, Fla.) | 2015 | PMID: 25596455 |
Intrafamilial variable phenotypic expression of a CIAS1 mutation: from Muckle-Wells to chronic infantile neurological cutaneous and articular syndrome. | Hentgen V | The Journal of rheumatology | 2005 | PMID: 15801036 |
Mutation of a new gene encoding a putative pyrin-like protein causes familial cold autoinflammatory syndrome and Muckle-Wells syndrome. | Hoffman HM | Nature genetics | 2001 | PMID: 11687797 |
Cold hypersensitivity. | Shepard MK | Birth defects original article series | 1971 | PMID: 5173311 |
Text-mined citations for rs121908146 ...
HelpRecord last updated Nov 03, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.