ClinVar Genomic variation as it relates to human health

The FH c.521C>G (p.Pro174Arg) missense variant has been reported in three studies in which it is found in a compound heterozygous state in four individuals with fumarate hydratase, two of whom were siblings with a severe phenotype who carried the p.Pro174Arg variant and a deletion in the FH gene (Alam et al. 2003; Mroch et al. 2012; Kimonis et al. 2012). Control data are unavailable for the p.Pro174Arg variant, which is reported at a frequency of 0.00045 in the African American population of the Exome Sequencing Project but this is based on two alleles only in a region of good sequencing coverage so the variant is presumed rare. Functional studies in patient skin fibroblasts and cells lines showed that the variant resulted in between 13 - 25% fumarase activity compared to controls (Alam et al. 2003; Kimonis et al. 2012). Based on the evidence the p.Pro174Arg variant is classified as likely pathogenic for fumarate hydratase deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Application of AMCG guidelines 2015. Used other ClinVar submission evidence where relevant. Loss of heterozygosity in tumours or immunohistochemistry abnormalities considered functional evidence of pathogenicity.

This variant has been previously reported as a compound heterozygous and homozygous change in patients with fumarase deficiency (PMID: 12761039, 22069215, 16575891). Functional studies showed that the c.521C>G (p.Pro174Arg) variant resulted in an increase in excretion of fumaric acid and reduced fumarase activity in fibroblast cells (PMID: 22595425, 12761039, 16575891). The c.521C>G (p.Pro174Arg) variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.002% (7/282696) and is absent in the homozygous state, thus is presumed to be rare. The c.521C>G (p.Pro174Arg) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.521C>G (p.Pro174Arg) variant is classified as Pathogenic.

The frequency of this variant in the general population, 0.000054 (7/129060 chromosomes, http://gnomad.broadinstitute.org), is consistent with pathogenicity. This variant has been detected in individuals with fumarase deficiency, who were compound heterozygous and homozygous for the variant (PMID: 22069215 (2012), 16575891 (2006), 12761039 (2003)). Additionally, the variant was shown to result in reduced enzyme activity (PMID: 12761039 (2003)). Based on the available information, this variant is classified as pathogenic.

The FH c.521C>G (p.Pro174Arg) missense change has a maximum subpopulation frequency of 0.0054% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a deleterious effect on protein function, but to our knowledge these predictions have not been confirmed by functional studies which interrogate this variant alone. This variant has been reported to be in trans with pathogenic variants in FH in individuals affected with autosomal recessive fumarase deficiency (PMID: 12761039, 22069215) and has been reported as homozygous in an individual with mild fumarase deficiency (PMID: 16575891). To our knowledge, this variant has not been reported in individuals with hereditary leiomyomatosis and renal cell cancer (HLRCC) and individuals identified to be heterozygous for this variant did not have a personal or family history of HLRCC (PMID: 12761039, 16575891, 22069215). This variant is also known as c.392C>G (p.Pro131Arg) in the literature. In summary, this variant meets criteria to be classified as pathogenic with respect to autosomal recessive FH deficiency, and of uncertain significance with respect to autosomal dominant HLRCC.

The p.P174R pathogenic mutation (also known as c.521C>G), located in coding exon 4 of the FH gene, results from a C to G substitution at nucleotide position 521. The proline at codon 174 is replaced by arginine, an amino acid with dissimilar properties. This alteration has been observed in multiple individuals with fumarate hydratase (FH) deficiency in conjunction with another mutation in trans or in a homozygous state (Alam NA et al. Hum. Mol. Genet. 2003 Jun;12:1241-52; Zeng WQ et al. Am. J. Med. Genet. A. 2006 May;140:1004-9; Mroch AR et al. Am. J. Med. Genet. A. 2012 Jan;158A:155-8; Ryder B et al. JIMD Rep 2018 Oct;40:77-83). In addition, patients with FH deficiency and this alteration have shown reduced enzyme activity (13-36%) relative to controls (Pollard PJ et al. Hum. Mol. Genet. 2005 Aug;14:2231-9; Zeng WQ et al. Am. J. Med. Genet. A. 2006 May;140:1004-9; Kimonis VE et al. Mol. Genet. Metab. 2012 Sep;107:241-2). Of note, this alteration is also designated as p.P131R in published literature. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this alteration is classified as a disease-causing mutation in association with autosomal recessive FH deficiency when present along with a second pathogenic or likely pathogenic variant on the other allele; however, the association of this alteration with HLRCC is unlikely.

Observed multiple times with a pathogenic variant on the opposite allele (in trans) and in the homozygous state in unrelated patients with fumarate hydratase deficiency, including those whose lymphocytes demonstrated decreased fumarate hydratase activity (PMID: 12761039, 15987702, 16575891, 22595425, 22069215, 29052812); Heterozygous individuals in the literature and at GeneDx with this variant have not been reported to have features of hereditary leiomyomatosis and renal cell cancer (HLRCC); therefore, its association with HLRCC is uncertain (PMID: 22069215, 16575891); Published functional studies demonstrate reduced rate of conversion of fumarate and malate in vitro (PMID: 37255402); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as p.(Pro131Arg); This variant is associated with the following publications: (PMID: 29909963, 20549362, 16029320, 16575891, 26580448, 31831373, 25637381, 21445611, 22069215, 22595425, 12761039, 15987702, 29052812, 16237213, 29086383, 11865300, 32191290, 34308104, 37255402)

This sequence change replaces proline, which is neutral and non-polar, with arginine, which is basic and polar, at codon 174 of the FH protein (p.Pro174Arg). This variant is present in population databases (rs199822819, gnomAD 0.006%). This missense change has been observed in individual(s) with autosomal recessive fumarase deficiency (PMID: 12761039, 16575891, 22069215). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 392C>G (Pro131Arg). ClinVar contains an entry for this variant (Variation ID: 29705). 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) performed at Invitae indicates that this missense variant is expected to disrupt FH protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects FH function (PMID: 12761039, 16575891, 22595425). For these reasons, this variant has been classified as Pathogenic.

Variant summary: FH c.521C>G (p.Pro174Arg) results in a non-conservative amino acid change located in the Fumarate lyase, N-terminal domain (IPR022761) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 2e-05 in 251304 control chromosomes. c.521C>G has been reported in the literature in multiple bi-allelelic individuals affected with Fumarate Hydratase Deficiency (examples: Alam_2003, Zeng_2006, Kimonis_2012, Mroch_2012, Ryder_2017). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 12761039, 29052812, 22595425, 16575891, 22069215). ClinVar contains an entry for this variant (Variation ID: 29705). Based on the evidence outlined above, the variant was classified as pathogenic.

The FH c.521C>G variant is predicted to result in the amino acid substitution p.Pro174Arg. This variant has been reported in the compound heterozygous and homozygous states in individuals with autosomal recessive fumarase deficiency and may lead to a mild clinical presentation (Alam et al. 2003. PubMed ID: 12761039; Zeng et al. 2006. PubMed ID: 16575891; Mroch et al. 2012. PubMed ID: 22069215; Kimonis et al. 2012. PubMed ID: 22595425). Parents heterozygous for this variant in the aforementioned studies did not exhibit HLRCC phenotypes. This variant has been reported in a patient with bilateral pheochromocytoma, but the individual also harbored a stop loss MAX gene variant (Whitworth et al. 2018. PubMed ID: 29909963). Biochemical testing from this variant leads to increased fumaric acid, and in vitro analysis showed reduced enzyme activity (Zeng et al. 2006. PubMed ID: 16575891; Mroch et al. 2012. PubMed ID: 22069215; Kimonis et al. 2012. PubMed ID: 22595425). This variant is also known in the literature as P131R. We classify this variant as pathogenic.

Variant interpreted as Pathogenic and reported on 05-13-2019 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.