Description
The MEFV p.Arg408Gln variant is a well-studied variant in association with Familial Mediterranean Fever (FMF) and has been identified in 159 of 8198 proband chromosomes from multiple patients with the FMF phenotype (freq=0.019), however the role of this variant in disease is unclear (Cazeneuve_1999_PMID:10364520; Bonyadi_2009_PMID: 19863562; Migita_2014_PMID:24797171; Tsuchiya-Suzuki_2009_PMID:19531756; Migita_2012_PMID:22467954; De Pieri_2015_PMID:25866490; Lainka_2012_PMID:22903357; Berdeli_2011_PMID:21413889; Migita_2016_PMID:27473114). The variant was reported in dbSNP (ID: rs11466024), LOVD 3.0 and ClinVar (classified in relation to FMF as benign [Prevention Genetics, 2017], likely benign [Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics, 2015], Likely pathogenic [EGL Genetic Diagnostics, 2017], Pathogenic [GeneReviews, 2016], Uncertain significance [GeneDx 2017; Praxis fuer Humar 2016; Invitae 2018; Integrated Genetics/Laboratory Corporation of America 2016; OMIM 2013; Integrated Genetics/Laboratory Corporation of America 2015]). The variant was not identified in the Cosmic database. The variant was identified in control databases in 3771 of 282186 chromosomes (53 homozygous) at a frequency of 0.013364 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 1072 of 19934 chromosomes (freq: 0.05378), Ashkenazi Jewish in 301 of 10342 chromosomes (freq: 0.0291), South Asian in 455 of 30606 chromosomes (freq: 0.01487), European (Finnish) in 363 of 25074 chromosomes (freq: 0.01448), Other in 94 of 7204 chromosomes (freq: 0.01305), European (non-Finnish) in 1175 of 128692 chromosomes (freq: 0.00913), Latino in 208 of 35416 chromosomes (freq: 0.005873), and African in 103 of 24918 chromosomes (freq: 0.004134). The R408Q variant is often found as a complex allele with the MEFV P369S variant. Bonyadi et al. (2009) identified the R408Q variant in 7/524 Azeri Turkish FMF patients as a complex allele with P369S; 4 of these patients were also compound heterozygous for another MEFV variant (Bonyadi_2009_PMID: 19863562). Migita et al. (2014) also identified the variant as a complex allele with P369S variant in 9/178 patients with typical FMF and 28/133 patients with atypical FMF; in 8 of these typical FMF and 15 of these atypical FMF patients the variant was present in the compound heterozygous state with at least one other MEFV variant (Migita_2014_PMID:24797171). A family with a severe autoinflammatory phenotype underwent testing of a 120 gene inflammasome-related panel which revealed a P369S/R408Q complex allele in the MEFV gene inherited from the father and found in both affected children as well as a T577A in the MEFV gene inherited from the affected mother and also found in both affected children (Stoffels_2014_PMID:23505238). Ryan et al. (2010) identified 35/40 symptomatic and 4 asymptomatic FMF family members with the R408Q/P369S complex allele. Functional studies of these variants did not demonstrate a significant difference from the wildtype in the ability of pyrin to bind to PSTPIP1, therefore the role of these variants in FMF and their potential functional impact is not known (Ryan_2010_PMID: 19934105). The variant occurs outside of the splicing consensus sequence however 3 of 4 in silico or computational prediction software programs (MaxEntScan, NNSPLICE, GeneSplicer) predict the creation of a new 5’ splice site. The p.Arg408 residue is not highly conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance, although we would suggest that this variant may be a low penetrant allele that can contribute to FMF in an autosomal recessive manner.
| # | Sample | Method | Observation |
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| Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
|---|
| 1 | unknown | yes | not provided | not provided | not provided | | not provided | not provided | not provided | not provided |
