ClinVar Miner

Submissions for variant NM_000243.2(MEFV):c.442G>C (p.Glu148Gln) (rs3743930)

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Total submissions: 17
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000513398 SCV000227072 pathogenic not provided 2017-09-27 criteria provided, single submitter clinical testing
GeneDx RCV000513398 SCV000279030 uncertain significance not provided 2018-10-15 criteria provided, single submitter clinical testing The E148Q variant in exon 2 of the MEFV gene has been described in individuals from many different ethnic backgrounds, and has been identified on 24% of FMF chromosomes that do not have a pathogenic variant in the most commonly mutated exon 10 (Bernot et al., 1998; Masters et al., 2009). However, a recent meta-analysis reported that the E148Q variant was present in 58/824 FMF alleles (7.0%) and in 163/2802 control alleles (5.8%) (Marek-Yagel et al., 2009). Therefore, it is currently unclear if E148Q is a pathogenic variant with low penetrance and mild symptoms, or a benign variant due to its similar frequency among patients and controls.
PreventionGenetics,PreventionGenetics RCV000218652 SCV000303125 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000002651 SCV000396780 likely benign Familial Mediterranean fever 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000218652 SCV000604166 benign not specified 2018-08-01 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000513398 SCV000608745 likely benign not provided 2017-04-30 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000218652 SCV000696072 uncertain significance not specified 2019-04-17 criteria provided, single submitter clinical testing Variant summary: MEFV c.442G>C (p.Glu148Gln) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. While the pathogenicity of this variant remains controversial, there have been several studies of symptomatic patients in certain ethnic backgrounds. The variant allele was found at a frequency of 0.072 in 236468 control chromosomes (gnomAD and publications), including 2070 homozygotes, well above the ACMG guideline of 5% threshold for an allele, strongly suggesting this variant lies in the benign spectrum. Particularly, this variant was found at a frequency of 28% in Asian population (East and South Asian) in gnomAD including 2013 homozygous occurrences. The population-based studies, therefore, strongly supports the hypothesis that E148Q is a benign polymorphism and not a disease-causing mutation. But there are numerous studies that associate the p.E148Q variant with FMF in certain ethnic backgrounds and report that it is a low penetrance pathogenic variant in specific genetic backgrounds (Ben-Chetrit_2000, Tchernitchko_2003). Apart from Asian population, it is relatively rare in other control populations: frequencies are in the range of 2% in European and African cohorts of gnomAD. This variant is predominant in Ashkenazi and Iraqi Jews, Armenians, and Turks, and has been associated with a generally mild form of FMF (Aksentijevich_1999,Tchernitchko_2003). This variant is regarded as one of the five mutations (p.Met680Ile (G>C), p.Met694Val, p.Met694Ile (G>T), and p.Val726Ala on exon 10, and p.Glu148Gln) that explain 85% of FMF cases in Middle East. In multiple unrelated patients, this variant also has been reported to be in cis with a pathogenic variant including V726A, M694V, M694I (Bernot_1998, Topaloglu_2005, Aksentijevich_1999). It is worth noting that the majority of publications citing this variant in FMF cohorts do not do comprehensive MEFV analysis, thus pathogenic variants may have been missed, which would explain the similar observed allele frequencies in patients and unaffected controls. 1/5 splice-site tools predicts a gain of cryptic splicing donor site, and ESEfinder predicts the addition of a SRp40 binding motif as well as minor changes to other binding motifs; however, the significance of these predictions has not been supported with functional studies. Recently, the SHARE (Single Hub and Access point for pediatric Rheumatology in Europe) initiative has developed evidence-based recommendations for genetic diagnosis of FMF and according to these recommendations, the E148Q variant is common, of unknown pathogenic significance and, as the only MEFV variant, does not support the genetic diagnosis of FMF. One publication reports this variant have less suppression on IL-8 secretion in cells compared to WT (Sugiyama_2014). Eight clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (1xpathogenic, 4xVUS, 3x likely benign). Taken together, the p.Glu148Gln variant could be very low penetrant pathogenic variant in certain genetic as well as ethnic backgrounds; however additional information is needed to fully assess its clinical significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
Invitae RCV000002651 SCV000753982 likely benign Familial Mediterranean fever 2020-01-22 criteria provided, single submitter clinical testing
Department of Genetics,Sultan Qaboos University Hospital, Oman RCV000761446 SCV000891531 uncertain significance Familial mediterranean fever, autosomal dominant 2017-12-30 criteria provided, single submitter curation
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768024 SCV000898827 uncertain significance Familial Mediterranean fever; Familial mediterranean fever, autosomal dominant 2019-11-19 criteria provided, single submitter clinical testing MEFV NM_000243.2 exon 2 p.Glu148Gln (c.442G>C): This variant has been well reported in the literature and identified in several individuals with Familial Mediteranean Fever (FMF) as homozygous, compound heterozygous or compound heterozygous as part of a complex allele containing this variant and p.Val726Ala, with the latter two found in trans with a different pathogenic variant (Bernot 1998 PMID:9668175, Kogan 2001 PMID:11484206, Gershoni-Baruch 2002 PMID:11938447). However, several publications claim that this variant is a benign polymorphism, suggesting equal incidence of this variant in affected individuals and control populations (Ben-Chetrit 2000 PMID:10737995, Tchernitchko 2003 PMID:12955725, Zaks 2003 PMID:12929299, Marek-Yagel 2009 PMID:19820229). A GeneReviews entry for FMF also notes the discrepant interpretation of this variant (Shohat 2016 PMID:20301405). This variant is present in 3% (5347/18284) of East Asian alleles, including 779 homozygotes, in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs3743930). This frequency is present at similar percentages among alleles of other ethnicities as well. This variant is present in ClinVar (Variation ID:2542). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000002651 SCV000930490 likely benign Familial Mediterranean fever 2019-04-27 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000513398 SCV001134282 uncertain significance not provided 2019-02-08 criteria provided, single submitter clinical testing
Mendelics RCV000002651 SCV001139889 benign Familial Mediterranean fever 2019-05-28 criteria provided, single submitter clinical testing
OMIM RCV000002651 SCV000022809 uncertain significance Familial Mediterranean fever 2002-01-01 no assertion criteria provided literature only
Integrated Genetics/Laboratory Corporation of America RCV000002651 SCV000052848 uncertain significance Familial Mediterranean fever 2015-10-05 no assertion criteria provided clinical testing
GeneReviews RCV000002651 SCV000484959 uncertain significance Familial Mediterranean fever 2016-12-15 no assertion criteria provided literature only
GenomeConnect, ClinGen RCV000002651 SCV000606900 not provided Familial Mediterranean fever no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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