ClinVar Genomic variation as it relates to human health
NM_000243.3(MEFV):c.443A>T (p.Glu148Val)
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.
Likely pathogenic(1); Uncertain significance(7); Benign(2); Likely benign(1)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_000243.3(MEFV):c.443A>T (p.Glu148Val)
Variation ID: 2554 Accession: VCV000002554.44
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 16p13.3 16: 3254625 (GRCh38) [ NCBI UCSC ] 16: 3304625 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
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 Apr 4, 2013 Oct 20, 2024 Apr 29, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_000243.3:c.443A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000234.1:p.Glu148Val missense NM_001198536.2:c.277+1686A>T intron variant NC_000016.10:g.3254625T>A NC_000016.9:g.3304625T>A NG_007871.1:g.7003A>T LRG_190:g.7003A>T LRG_190t1:c.443A>T LRG_190p1:p.Glu148Val O15553:p.Glu148Val - Protein change
- E148V
- Other names
- -
- Canonical SPDI
- NC_000016.10:3254624:T:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
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.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
-
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00008
Exome Aggregation Consortium (ExAC) 0.00010
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
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. |
|||
MEFV | No evidence available | No evidence available |
GRCh38 GRCh37 |
956 | 1257 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
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
Help
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
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Conflicting interpretations of pathogenicity (5) |
criteria provided, conflicting classifications
|
Feb 8, 2023 | RCV000002663.17 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
|
Apr 29, 2024 | RCV000415966.23 | |
Uncertain significance (2) |
criteria provided, multiple submitters, no conflicts
|
Dec 19, 2022 | RCV000216721.14 | |
Uncertain significance (1) |
criteria provided, single submitter
|
Apr 28, 2022 | RCV002482818.2 | |
Benign (1) |
criteria provided, single submitter
|
Feb 8, 2023 | RCV003125826.2 | |
Uncertain significance (1) |
criteria provided, single submitter
|
Dec 1, 2017 | RCV002262552.4 | |
Conflicting interpretations of pathogenicity (2) |
criteria provided, conflicting classifications
|
Sep 30, 2023 | RCV003125825.4 |
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
Help
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
Help
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. |
|
---|---|---|---|---|---|
Uncertain significance
(Oct 30, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV001156673.1
First in ClinVar: Feb 09, 2020 Last updated: Feb 09, 2020 |
Comment:
The MEFV c.443A>T; p.Glu148Val variant (rs104895076), is reported in the literature in the heterozygous, compound heterozygous, and homozygous state in individuals with a variety of … (more)
The MEFV c.443A>T; p.Glu148Val variant (rs104895076), is reported in the literature in the heterozygous, compound heterozygous, and homozygous state in individuals with a variety of symptoms, ranging from no symptoms to juvenile idiopathic arthritis to familial Mediterranean fever (Comak 2013, Dogan 2013, Dogan 2015, Giaglis 2007, Medlej-Hashim 2002, Sandhya 2017). This variant is reported in ClinVar (Variation ID: 2554), and is found in the South Asian population with an allele frequency of 0.043% (13/30,272 alleles) in the Genome Aggregation Database. The glutamic acid at codon 148 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Due to conflicting phenotype information, the clinical significance of the p.Glu148Val variant is uncertain at this time. References: Comak E et al. MEFV gene mutations in Turkish children with juvenile idiopathic arthritis. Eur J Pediatr. 2013 Aug;172(8):1061-7. Dogan CS et al. Prevalence and significance of the MEFV gene mutations in childhood Henoch-Schonlein purpura without FMF symptoms. Rheumatol Int. 2013 Feb;33(2):377-80. Dogan H et al. Familial Mediterranean fever gene mutations in north-eastern part of Anatolia with special respect to rare mutations. Gene. 2015 Sep 1;568(2):170-5. Giaglis S et al. MEFV alterations and population genetics analysis in a large cohort of Greek patients with familial Mediterranean fever. Clin Genet. 2007 May;71(5):458-67. Medlej-Hashim M et al. Familial Mediterranean fever: the potential for misdiagnosis of E148V using the E148Q usual RFLP detection method. Clin Genet. 2002 Jan;61(1):71-3. Sandhya P et al. Egyptian tale from India: application of whole-exome sequencing in diagnosis of atypical familial Mediterranean fever. Int J Rheum Dis. 2017 Nov;20(11):1770-1775. (less)
|
|
Uncertain significance
(Dec 01, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Autoinflammatory syndrome
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002543765.1
First in ClinVar: Jul 09, 2022 Last updated: Jul 09, 2022 |
|
|
Uncertain significance
(Apr 28, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Familial Mediterranean fever, autosomal dominant
Familial Mediterranean fever Acute febrile neutrophilic dermatosis
Affected status: unknown
Allele origin:
unknown
|
Fulgent Genetics, Fulgent Genetics
Accession: SCV002786056.1
First in ClinVar: Dec 31, 2022 Last updated: Dec 31, 2022 |
|
|
Uncertain significance
(Dec 19, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000052849.6
First in ClinVar: Apr 04, 2013 Last updated: Jan 15, 2023 |
Comment:
Variant summary: MEFV c.443A>T (p.Glu148Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Variant summary: MEFV c.443A>T (p.Glu148Val) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. A recently reported in-silico ensemble method for predicting pathogenicity of missense variants (Rare Exome Variant Ensemble Learner, REVEL) predicted a computed classification for this variant as likely pathogenic (Accetturo_2020). The variant allele was found at a frequency of 7.7e-05 in 235044 control chromosomes (gnomAD and publications). This frequency is not higher than expected for a pathogenic variant in MEFV causing Familial Mediterranean Fever (7.7e-05 vs 0.022), allowing no conclusion about variant significance. Following a comprehensive and conservative assessment of literature spanning over thirteen years (2007-2020), c.443A>T, has been reported in the literature in a homozygous/compound heterozygous genotype in multiple individuals affected with Familial Mediterranean Fever (example, Giaglis_2007, Ibrahim_2015, Lachmann_2006, Cekin_2017, Sandhya_2017, Gumus_2018, Bozgeyik_2020, Tanatar_2020). Numerous publications also reported affected individuals lacking a second allele. In addition, the variant has also been reported in asymptomatic individuals. At-least one co-occurrence in cis with another pathogenic MEFV variant (p.M694V Tchernitchko 2003) has been ascertained in the context of this evaluation. Variable reports of the extent of genotyping and lack of clearly defined phase information (i.e., presumed trans versus cis co-occurrence) confound an accurate assessment from the ascertained literature. These data indicate that the variant may be associated with disease in some genetic backgrounds. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six ClinVar submissions from clinical diagnostic laboratories (evaluations after 2014) cite the variant as "uncertain significance." Some submitters cite overlapping evidence utilized in the context of this evaluation. Therefore, due to the conflicting evidence outlined above, the variant has been classified as VUS-possibly pathogenic. (less)
|
|
Uncertain significance
(Aug 09, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Familial Mediterranean fever
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV001412934.2
First in ClinVar: Jul 16, 2020 Last updated: Feb 07, 2023 |
Comment:
This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 148 of the MEFV protein … (more)
This sequence change replaces glutamic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 148 of the MEFV protein (p.Glu148Val). This variant is present in population databases (rs104895076, gnomAD 0.04%). This missense change has been observed in individual(s) with familial mediterranean fever (PMID: 17489852, 24469716, 28211254, 28483595, 29735907). ClinVar contains an entry for this variant (Variation ID: 2554). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. (less)
|
|
Uncertain significance
(Sep 30, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Familial Mediterranean fever, autosomal dominant
Affected status: unknown
Allele origin:
unknown
|
Baylor Genetics
Accession: SCV004194413.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
|
|
Uncertain significance
(Apr 01, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV000493691.27
First in ClinVar: Jan 30, 2017 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
|
|
Benign
(Feb 08, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Familial Mediterranean fever, autosomal dominant
Affected status: unknown
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV003802371.1
First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023 |
|
|
Likely benign
(Feb 08, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Familial Mediterranean fever
Affected status: unknown
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV003802370.1
First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023 |
|
|
Benign
(Feb 08, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Acute febrile neutrophilic dermatosis
Affected status: unknown
Allele origin:
germline
|
Genome-Nilou Lab
Accession: SCV003802372.1
First in ClinVar: Feb 18, 2023 Last updated: Feb 18, 2023 |
|
|
Likely pathogenic
(Apr 29, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000279032.9
First in ClinVar: May 29, 2016 Last updated: Sep 16, 2024 |
Comment:
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: 25449140, … (more)
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: 25449140, 31411330, 23289470, 23588594, 28597968, 28483595, 29735907, 26585190, 30783801, 30874249, 30915208, 29756710, 28211254, 27170062, 34426522, 26247045, 35358658, 33576586, 26003477, 32199921, 22451026) (less)
|
|
Pathogenic
(Jan 01, 2002)
|
no assertion criteria provided
Method: literature only
|
FAMILIAL MEDITERRANEAN FEVER
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000022821.2
First in ClinVar: Apr 04, 2013 Last updated: Jun 15, 2020 |
Comment on evidence:
Medlej-Hashim et al. (2002) described the glu148-to-val mutation (E148V) in 1 Lebanese patient with familial Mediterranean fever (FMF; 249100). They pointed out that the usual … (more)
Medlej-Hashim et al. (2002) described the glu148-to-val mutation (E148V) in 1 Lebanese patient with familial Mediterranean fever (FMF; 249100). They pointed out that the usual RFLP detection method used for E148Q (608107.0005), which may represent a polymorphism or at the most a weakly pathogenic allele, gives the same restriction pattern as does E148V. When AvaI restriction enzyme is used the 2 mutations cause the same pattern; different patterns are created by E148Q and E148V when MvaI enzyme is used. (less)
|
|
Uncertain significance
(Sep 16, 2020)
|
no assertion criteria provided
Method: clinical testing
|
Familial Mediterranean fever
Affected status: unknown
Allele origin:
germline
|
Natera, Inc.
Accession: SCV001452090.1
First in ClinVar: Jan 02, 2021 Last updated: Jan 02, 2021 |
|
|
not provided
(-)
|
no classification provided
Method: not provided
|
Familial Mediterranean fever
Affected status: not provided
Allele origin:
unknown
|
Unité médicale des maladies autoinflammatoires, CHRU Montpellier
Accession: SCV000115872.1
First in ClinVar: Mar 06, 2014 Last updated: Mar 06, 2014 |
|
|
click to load more click to collapse |
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 |
---|---|---|---|---|
Next-generation screening of a panel of genes associated with periodic fever syndromes in patients with Familial Mediterranean Fever and their clinical characteristics. | Bozgeyik E | Genomics | 2020 | PMID: 32199921 |
Performance of Tel-Hashomer, Livneh, pediatric and new Eurofever/PRINTO classification criteria for familial Mediterranean fever in a referral center. | Tanatar A | Rheumatology international | 2020 | PMID: 31646357 |
Improvement of MEFV gene variants classification to aid treatment decision making in familial Mediterranean fever. | Accetturo M | Rheumatology (Oxford, England) | 2020 | PMID: 31411330 |
The Frequency of MEFV Gene Mutations and Genotypes in Sanliurfa Province, South-Eastern Region of Turkey, after the Syrian Civil War by Using Next Generation Sequencing and Report of a Novel Exon 4 Mutation (I423T). | Gumus E | Journal of clinical medicine | 2018 | PMID: 29735907 |
Genetic epidemiology of familial Mediterranean fever through integrative analysis of whole genome and exome sequences from Middle East and North Africa. | Koshy R | Clinical genetics | 2018 | PMID: 28597968 |
A web-based collection of genotype-phenotype associations in hereditary recurrent fevers from the Eurofever registry. | Papa R | Orphanet journal of rare diseases | 2017 | PMID: 29047407 |
MEFV mutations and their relation to major clinical symptoms of Familial Mediterranean Fever. | Cekin N | Gene | 2017 | PMID: 28483595 |
Egyptian tale from India: application of whole-exome sequencing in diagnosis of atypical familial Mediterranean fever. | Sandhya P | International journal of rheumatic diseases | 2017 | PMID: 28211254 |
Study of the association of IL-1β and IL-1RA gene polymorphisms with occurrence and severity of Familial Mediterranean fever. | Ibrahim JN | European journal of medical genetics | 2015 | PMID: 26585190 |
Febrile seizures in children with familial Mediterranean fever: Coincidence or association? | Çomak E | European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society | 2015 | PMID: 26028444 |
Familial Mediterranean fever gene mutations in north-eastern part of Anatolia with special respect to rare mutations. | Dogan H | Gene | 2015 | PMID: 26003477 |
Screening of common and novel familial mediterranean fever mutations in south-east part of Turkey. | Oztuzcu S | Molecular biology reports | 2014 | PMID: 24469716 |
Results from a multicentre international registry of familial Mediterranean fever: impact of environment on the expression of a monogenic disease in children. | Ozen S | Annals of the rheumatic diseases | 2014 | PMID: 23463692 |
MEFV gene mutations in Turkish children with juvenile idiopathic arthritis. | Comak E | European journal of pediatrics | 2013 | PMID: 23588594 |
Prevalence and significance of the MEFV gene mutations in childhood Henoch-Schönlein purpura without FMF symptoms. | Dogan CS | Rheumatology international | 2013 | PMID: 22451026 |
Familial Mediterranean fever in Germany: epidemiological, clinical, and genetic characteristics of a pediatric population. | Lainka E | European journal of pediatrics | 2012 | PMID: 22903357 |
Comprehensive analysis of a large-scale screen for MEFV gene mutations: do they truly provide a "heterozygote advantage" in Turkey? | Berdeli A | Genetic testing and molecular biomarkers | 2011 | PMID: 21413889 |
MEFV alterations and population genetics analysis in a large cohort of Greek patients with familial Mediterranean fever. | Giaglis S | Clinical genetics | 2007 | PMID: 17489852 |
Clinical and subclinical inflammation in patients with familial Mediterranean fever and in heterozygous carriers of MEFV mutations. | Lachmann HJ | Rheumatology (Oxford, England) | 2006 | PMID: 16403826 |
Familial Mediterranean fever (FMF) in Turkey: results of a nationwide multicenter study. | - | Medicine | 2005 | PMID: 15643295 |
In silico prediction of the deleterious effect of a mutation: proceed with caution in clinical genetics. | Tchernitchko D | Clinical chemistry | 2004 | PMID: 15502081 |
Familial Mediterranean fever. | Konstantopoulos K | The New Zealand medical journal | 2004 | PMID: 15475974 |
Genetic testing for familial Mediterranean fever in Austria by means of reverse-hybridization teststrips. | Oberkanins C | Clinical chemistry | 2003 | PMID: 14578333 |
Clinical evaluation of a reverse hybridization assay for the molecular detection of twelve MEFV gene mutations. | Tchernitchko D | Clinical chemistry | 2003 | PMID: 14578331 |
Familial Mediterranean fever: the potential for misdiagnosis of E148V using the E148Q usual RFLP detection method. | Medlej-Hashim M | Clinical genetics | 2002 | PMID: 11903360 |
click to load more click to collapse |
Text-mined citations for rs104895076 ...
HelpRecord last updated Oct 20, 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.