ClinVar Genomic variation as it relates to human health
NM_001322934.2(NFKB2):c.2557C>T (p.Arg853Ter)
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_001322934.2(NFKB2):c.2557C>T (p.Arg853Ter)
Variation ID: 65385 Accession: VCV000065385.46
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 10q24.32 10: 102402138 (GRCh38) [ NCBI UCSC ] 10: 104161895 (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 Sep 18, 2013 Oct 20, 2024 Sep 25, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001322934.2:c.2557C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001309863.1:p.Arg853Ter nonsense NM_001077494.3:c.2557C>T NP_001070962.1:p.Arg853Ter nonsense NM_001261403.3:c.2557C>T NP_001248332.1:p.Arg853Ter nonsense NM_001288724.1:c.2557C>T NP_001275653.1:p.Arg853Ter nonsense NM_001322935.1:c.2431C>T NP_001309864.1:p.Arg811Ter nonsense NM_002502.6:c.2557C>T NP_002493.3:p.Arg853Ter nonsense NC_000010.11:g.102402138C>T NC_000010.10:g.104161895C>T NG_033874.2:g.13029C>T LRG_1347:g.13029C>T LRG_1347t1:c.2557C>T LRG_1347p1:p.Arg853Ter - Protein change
- R853*, R811*
- Other names
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- Canonical SPDI
- NC_000010.11:102402137: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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dominant_negative_variant; Sequence Ontology [ SO:0002052]
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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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NFKB2 | - | - |
GRCh38 GRCh37 |
549 | 693 | |
PSD | - | - |
GRCh38 GRCh37 |
66 | 93 |
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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Pathogenic (1) |
criteria provided, single submitter
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Dec 15, 2016 | RCV000055612.16 | |
Pathogenic (9) |
criteria provided, multiple submitters, no conflicts
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Sep 25, 2024 | RCV000077761.28 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Jul 15, 2022 | RCV001093426.29 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 1, 2019 | RCV001027606.9 | |
Pathogenic (1) |
criteria provided, single submitter
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Jan 9, 2020 | RCV001174741.9 |
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
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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
(Dec 15, 2016)
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criteria provided, single submitter
Method: clinical testing
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not specified
Affected status: unknown
Allele origin:
germline
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ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV000083837.2
First in ClinVar: Sep 18, 2013 Last updated: Sep 18, 2013 |
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Pathogenic
(Jan 01, 2019)
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criteria provided, single submitter
Method: research
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Inherited Immunodeficiency Diseases
Affected status: yes
Allele origin:
germline
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NIHR Bioresource Rare Diseases, University of Cambridge
Accession: SCV001190180.1
First in ClinVar: Mar 26, 2020 Last updated: Mar 26, 2020 |
Clinical Features:
Immunodeficiency (present)
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Pathogenic
(Jan 09, 2020)
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criteria provided, single submitter
Method: clinical testing
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Common variable immunodeficiency
Affected status: unknown
Allele origin:
germline
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Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001338047.1
First in ClinVar: Jun 22, 2020 Last updated: Jun 22, 2020 |
Comment:
Variant summary: NFKB2 c.2557C>T (p.Arg853X) results in a premature termination codon, and though it is not expected to cause nonsense mediated decay (NMD), it is … (more)
Variant summary: NFKB2 c.2557C>T (p.Arg853X) results in a premature termination codon, and though it is not expected to cause nonsense mediated decay (NMD), it is predicted to cause a truncation of the encoded protein. The variant was absent in 187640 control chromosomes (gnomAD). c.2557C>T has been reported in the literature in numerous individuals affected with Common Variable Immunodeficiency (e.g. Chen_2013, Klemann_2019). These data indicate that the variant is very likely to be associated with disease. Publications also reported experimental evidence evaluating an impact on protein function, and demonstrated that this C-terminal truncation indeed affects normal protein function (Chen_2013, Kuehn_2017). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. (less)
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Pathogenic
(Jan 21, 2020)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
Affected status: unknown
Allele origin:
germline
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Johns Hopkins Genomics, Johns Hopkins University
Accession: SCV001425340.1
First in ClinVar: Aug 03, 2020 Last updated: Aug 03, 2020 |
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Pathogenic
(Sep 26, 2022)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
Affected status: yes
Allele origin:
unknown
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Molecular Genetics Laboratory - Diagnostics Genetics, LabPLUS - Auckland City Hospital
Accession: SCV002575024.1
First in ClinVar: Oct 22, 2022 Last updated: Oct 22, 2022 |
Clinical Features:
CVID (present)
Age: 0-9 years
Sex: female
Ethnicity/Population group: Maori
Geographic origin: New Zealand
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Pathogenic
(Jul 15, 2022)
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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: SCV002549308.2
First in ClinVar: Jul 23, 2022 Last updated: Mar 04, 2023 |
Comment:
Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 48 amino acids are lost, and other loss-of-function variants have been … (more)
Nonsense variant in the C-terminus predicted to result in protein truncation, as the last 48 amino acids are lost, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (HGMD); In vitro assays demonstrated that R853X has a dominant negative effect (Kuehn et al., 2017); Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 24702956, 25605273, 27577878, 28778864, 28983403, 29225085, 30941118, 30078247, 28919517, 30267444, 24140114, 25524009, 30500415, 29952021, 32135276, 32499645, 32888943, 32694887) (less)
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Pathogenic
(Feb 23, 2023)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
Affected status: yes
Allele origin:
unknown
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3billion
Accession: SCV003841639.1
First in ClinVar: Mar 18, 2023 Last updated: Mar 18, 2023 |
Comment:
The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function … (more)
The variant is not observed in the gnomAD v2.1.1 dataset. This variant was predicted to result in a loss or disruption of normal protein function through protein truncation. Multiple pathogenic variants are reported in the predicted truncated region. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000065385 / PMID: 24140114). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. (less)
Clinical Features:
Tip-toe gait (present) , Skeletal myopathy (present) , Distal muscle weakness (present) , Difficulty walking (present) , Hypothyroidism (present) , Elevated circulating creatine kinase concentration … (more)
Tip-toe gait (present) , Skeletal myopathy (present) , Distal muscle weakness (present) , Difficulty walking (present) , Hypothyroidism (present) , Elevated circulating creatine kinase concentration (present) (less)
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Pathogenic
(Sep 05, 2023)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
inherited
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Bioinformatics Unit, Institut Pasteur de Montevideo
Accession: SCV004031475.1
First in ClinVar: Sep 09, 2023 Last updated: Sep 09, 2023 |
Comment:
We found this variant in three affected family members and not present in an unaffected one.
Number of individuals with the variant: 3
Sex: male
Geographic origin: Uruguay
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Pathogenic
(Nov 18, 2023)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000773792.7
First in ClinVar: Oct 11, 2015 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Arg853*) in the NFKB2 gene. While this is not anticipated to result in nonsense mediated decay, … (more)
This sequence change creates a premature translational stop signal (p.Arg853*) in the NFKB2 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 48 amino acid(s) of the NFKB2 protein. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with NFKB2-related immunodeficiencies (PMID: 24702956, 25524009, 25605273). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 65385). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects NFKB2 function (PMID: 24140114, 28778864). For these reasons, this variant has been classified as Pathogenic. (less)
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Pathogenic
(Mar 17, 2024)
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criteria provided, single submitter
Method: research
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Immunodeficiency, common variable, 10
Affected status: unknown
Allele origin:
germline
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Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center
Accession: SCV004804996.2
First in ClinVar: Mar 30, 2024 Last updated: Apr 06, 2024 |
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Pathogenic
(Sep 25, 2024)
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criteria provided, single submitter
Method: clinical testing
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Immunodeficiency, common variable, 10
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
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Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV005328352.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Clinical Features:
Apraxia (present) , Memory impairment (present) , Alzheimer disease (present) , Recurrent infections (present) , Immunodeficiency (present) , Autoimmunity (present) , Generalized cerebral atrophy/hypoplasia (present) … (more)
Apraxia (present) , Memory impairment (present) , Alzheimer disease (present) , Recurrent infections (present) , Immunodeficiency (present) , Autoimmunity (present) , Generalized cerebral atrophy/hypoplasia (present) , Alopecia totalis (present) , Chronic sinusitis (present) , Abnormally slow thought process (present) , Elevated CSF neurofilament light chain concentration (present) , Impaired executive functioning (present) , Dementia (present) (less)
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Pathogenic
(Mar 01, 2018)
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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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CeGaT Center for Human Genetics Tuebingen
Accession: SCV001250394.26
First in ClinVar: May 12, 2020 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
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Pathogenic
(-)
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no assertion criteria provided
Method: research
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Combined variable immunodeficiency (CVID) with pituitary insufficiency (ACTH deficiency, sometimes with growth hormone or thyroid hormone deficiency)
Affected status: yes
Allele origin:
unknown
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Samuels research lab, Centre de Recherche du CHU Ste-Justine
Study: FORGE Canada
Accession: SCV000172088.1 First in ClinVar: Jan 28, 2015 Last updated: Jan 28, 2015
Comment:
Molecular characterization of rare pediatric disorders in Canada
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Number of individuals with the variant: 1
Geographic origin: Italy
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Pathogenic
(Dec 19, 2014)
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no assertion criteria provided
Method: literature only
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IMMUNODEFICIENCY, COMMON VARIABLE, 10
Affected status: not provided
Allele origin:
germline
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OMIM
Accession: SCV000109567.3
First in ClinVar: Dec 24, 2013 Last updated: Jan 31, 2019 |
Comment on evidence:
In a patient of northern European descent with common variable immunodeficiency-10 (CVID10; 615577), Chen et al. (2013) identified a heterozygous c.2557C-T transition in the NFKB2 … (more)
In a patient of northern European descent with common variable immunodeficiency-10 (CVID10; 615577), Chen et al. (2013) identified a heterozygous c.2557C-T transition in the NFKB2 gene, resulting in an arg853-to-ter (R853X) substitution. This patient was identified from a cohort of 33 individuals with CVID who were tested for variants in the NFKB2 gene. The mutation was not found in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases or in 50 control exomes. The unaffected mother did not carry the mutation; DNA from the father was unavailable. The mutation caused a truncation in the C terminus of the protein, removing the conserved phosphorylation sites required for activation of p100 to p52. Cell lines carrying the mutation lacked the phosphorylated signal observed in control cells. The mutant truncated protein could not be processed by the proteasome, resulting in reduced protein activation and nuclear translocation. In a boy with CVID10, Brue et al. (2014) identified a de novo heterozygous R853X mutation in the NFKB2 gene within the C-terminal NIK (MAP3K14; 604655) response domain. The patient also had hair loss and low ACTH; brain MRI showed a hypoplastic anterior pituitary. Functional studies of the variant were not performed. (less)
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Germline Functional Evidence
Functional
Help
The functional consequence of the variant, based on experimental evidence and provided by the submitter. consequence |
Method
Help
A brief description of the method used to determine the functional consequence of the variant. A citation for the method is included, when provided by the submitter. |
Result
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A brief description of the result of this method for 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
Help
This column includes more information supporting functional evidence for the germline classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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dominant_negative_variant
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Molecular Genetics Laboratory - Diagnostics Genetics, LabPLUS - Auckland City Hospital
Accession: SCV002575024.1
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Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Clinical and Immunological Phenotype of Patients With Primary Immunodeficiency Due to Damaging Mutations in NFKB2. | Klemann C | Frontiers in immunology | 2019 | PMID: 30941118 |
Anticytokine autoantibodies in a patient with a heterozygous NFKB2 mutation. | Ramakrishnan KA | The Journal of allergy and clinical immunology | 2018 | PMID: 29225085 |
Novel nonsense gain-of-function NFKB2 mutations associated with a combined immunodeficiency phenotype. | Kuehn HS | Blood | 2017 | PMID: 28778864 |
Defective natural killer-cell cytotoxic activity in NFKB2-mutated CVID-like disease. | Lougaris V | The Journal of allergy and clinical immunology | 2015 | PMID: 25605273 |
Mutations in NFKB2 and potential genetic heterogeneity in patients with DAVID syndrome, having variable endocrine and immune deficiencies. | Brue T | BMC medical genetics | 2014 | PMID: 25524009 |
Phevor combines multiple biomedical ontologies for accurate identification of disease-causing alleles in single individuals and small nuclear families. | Singleton MV | American journal of human genetics | 2014 | PMID: 24702956 |
Germline mutations in NFKB2 implicate the noncanonical NF-κB pathway in the pathogenesis of common variable immunodeficiency. | Chen K | American journal of human genetics | 2013 | PMID: 24140114 |
Text-mined citations for rs397514332 ...
HelpRecord last updated Nov 25, 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.