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A relatively common hypomorphic variant in WARS2 causes monogenic disease

      Keywords

      In this issue of Parkinsonism and Related Disorders, Dr. Škorvánek et al. describe 6 patients from 4 families with a rare autosomal recessive neurodevelopmental disease caused by biallelic mutations in the WARS2 gene [
      • Skorvanek M.
      • Rektorova I.
      • Mandemakers W.
      • Wagner M.
      • Steinfeld R.
      • Orec L.
      • Han V.
      • Pavelekova P.
      • Lackova A.
      • Kulcsarova K.
      • Ostrozovicova M.
      • Gdovinova Z.
      • Plecko B.
      • Brunet T.
      • Berutti R.
      • Kuipers D.J.S.
      • Boumeester V.
      • Havrankova P.
      • Tijssen M.A.J.
      • Kaiyrzhanov R.
      • Rizig M.
      • Houlden H.
      • Winkelmann J.
      • Bonifati V.
      • Zech M.
      • Jech R.
      WARS2 mutations cause dopa-responsive early-onset parkinsonism and progressive myoclonus ataxia.
      ]. WARS2 is a nuclear gene encoding mitochondrial tryptophanyl aminoacyl tRNA synthetase, which loads the amino acid tryptophan onto the specific tRNA for protein synthesis in mitochondria. The disease phenotype represents a mitochondriopathy, with a broad variety of movement disorders, neuropsychiatric manifestations, visual loss, leukoencephalopathy, intellectual disability and somatic phenotypes including cardiac and gastrointestinal manifestations, short stature, and dysmorphies.
      This disorder is very rare; Škorvánek et al. summarize information on 16 previously described patients with a disorder related with WARS2 mutations. We have recently found that one of our Swedish patients is compound heterozygous for WARS2 c.833T>G p.(Val278Gly) and c.938A>T p.(Lys313Met); reference NM_015836.3. This patient, now 22 years old, was born at term but was small for gestational age. Soon after birth, she had necrotizing enterocolitis, to which we hypothesize her genetic mitochondrial dysfunction might have been a contributing cause. She had neonatal seizures and has persistent epilepsy with generalized and complex partial seizures. She had increased muscle tone and limb tremor, difficulties to learn walking, and juvenile Parkinsonism that was clearly responsive to levodopa. She developed levodopa-induced dyskinesias. There was also cervical and truncal dystonia, a thoracolumbar scoliosis requiring surgical correction, and there were myoclonic jerks. Brain MRI showed thin corpus callosum, mildly reduced cerebral and cerebellar volume, and at age 6 years a transient juxtaventricular white matter hyperintensity. The same genotype had previously been described in two Swedish siblings with a similar disease phenotype [
      • Maffezzini C.
      • Laine I.
      • Dallabona C.
      • Clemente P.
      • Calvo-Garrido J.
      • Wibom R.
      • Naess K.
      • Barbaro M.
      • Falk A.
      • Donnini C.
      • Freyer C.
      • Wredenberg A.
      • Wedell A.
      Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.
      ], but families were not aware of any relatedness. One additional female patient with the recurrent p.(Trp13Gly) variant, in compound heterozygosity with the probably pathogenic c.487C>T p.(Leu163Phe) variant that is rare in gnomAD (0.0016%), had been reported from Portugal; the patient had mental retardation, tremor and dystonia that manifested at 2 years of age and progressed slowly [
      • Nogueira C.
      • Silva L.
      • Pereira C.
      • Vieira L.
      • Leao Teles E.
      • Rodrigues E.
      • Campos T.
      • Janeiro P.
      • Gaspar A.
      • Dupont J.
      • Bandeira A.
      • Martins E.
      • Magalhaes M.
      • Sequeira S.
      • Vieira J.P.
      • Santos H.
      • Vilarinho S.
      • Vilarinho L.
      Targeted next generation sequencing identifies novel pathogenic variants and provides molecular diagnoses in a cohort of pediatric and adult patients with unexplained mitochondrial dysfunction.
      ].
      Škorvánek et al.’s patients from Central European centers add important knowledge to the disorder's phenotype, which in their patients was milder, also including early-onset Parkinsonism responsive to levodopa, and myoclonus ataxia. While for many rare genetic disorders the cases examined and described first often are those with the most severe clinical manifestations, Škorvánek et al. describe an interesting genetic phenomenon in their patients as an explanation for their milder phenotype: All their 6 patients as well as 6 of the previously published cases [
      • Skorvanek M.
      • Rektorova I.
      • Mandemakers W.
      • Wagner M.
      • Steinfeld R.
      • Orec L.
      • Han V.
      • Pavelekova P.
      • Lackova A.
      • Kulcsarova K.
      • Ostrozovicova M.
      • Gdovinova Z.
      • Plecko B.
      • Brunet T.
      • Berutti R.
      • Kuipers D.J.S.
      • Boumeester V.
      • Havrankova P.
      • Tijssen M.A.J.
      • Kaiyrzhanov R.
      • Rizig M.
      • Houlden H.
      • Winkelmann J.
      • Bonifati V.
      • Zech M.
      • Jech R.
      WARS2 mutations cause dopa-responsive early-onset parkinsonism and progressive myoclonus ataxia.
      ,
      • Nogueira C.
      • Silva L.
      • Pereira C.
      • Vieira L.
      • Leao Teles E.
      • Rodrigues E.
      • Campos T.
      • Janeiro P.
      • Gaspar A.
      • Dupont J.
      • Bandeira A.
      • Martins E.
      • Magalhaes M.
      • Sequeira S.
      • Vieira J.P.
      • Santos H.
      • Vilarinho S.
      • Vilarinho L.
      Targeted next generation sequencing identifies novel pathogenic variants and provides molecular diagnoses in a cohort of pediatric and adult patients with unexplained mitochondrial dysfunction.
      ] carried one and the same recurring WARS2 variant, c.37T>G p.(Trp13Gly), combined in trans with another variant in the second WARS2 allele. Functional data show that p.(Trp13Gly) diminishes (but does not abate) transport of WARS2 protein into mitochondria [
      • Skorvanek M.
      • Rektorova I.
      • Mandemakers W.
      • Wagner M.
      • Steinfeld R.
      • Orec L.
      • Han V.
      • Pavelekova P.
      • Lackova A.
      • Kulcsarova K.
      • Ostrozovicova M.
      • Gdovinova Z.
      • Plecko B.
      • Brunet T.
      • Berutti R.
      • Kuipers D.J.S.
      • Boumeester V.
      • Havrankova P.
      • Tijssen M.A.J.
      • Kaiyrzhanov R.
      • Rizig M.
      • Houlden H.
      • Winkelmann J.
      • Bonifati V.
      • Zech M.
      • Jech R.
      WARS2 mutations cause dopa-responsive early-onset parkinsonism and progressive myoclonus ataxia.
      ]. Patients who were compound heterozygous for p.(Trp13Gly) and a missense variant developed symptoms at a mean of over 4 years of age, those with biallelic missense mutations at a mean of 6 months, but those with at least one truncating mutation (in compound heterozygosity with another, either p.[Trp13Gly] and missense) had symptoms from birth and may have had the most severe course of symptom progression (from Table in Ref. [
      • Skorvanek M.
      • Rektorova I.
      • Mandemakers W.
      • Wagner M.
      • Steinfeld R.
      • Orec L.
      • Han V.
      • Pavelekova P.
      • Lackova A.
      • Kulcsarova K.
      • Ostrozovicova M.
      • Gdovinova Z.
      • Plecko B.
      • Brunet T.
      • Berutti R.
      • Kuipers D.J.S.
      • Boumeester V.
      • Havrankova P.
      • Tijssen M.A.J.
      • Kaiyrzhanov R.
      • Rizig M.
      • Houlden H.
      • Winkelmann J.
      • Bonifati V.
      • Zech M.
      • Jech R.
      WARS2 mutations cause dopa-responsive early-onset parkinsonism and progressive myoclonus ataxia.
      ] and above information). In line with such a gene dosage effect, dependent on mutation type, Škorvánek et al. designate the p.(Trp13Gly) variant as a “hypomorphic variant”.
      The term “hypomorphic variant” is attributed to 1946 Nobel laureate Hermann J. Müller who used it to describe genetic variation that “works in the same direction […], but not so strongly” [
      • Muller H.J.
      Further studies on the nature and causes of gene mutations.
      ]. It is most readily explained for recessive disorders with a loss-of-function mechanism: In the classical model of recessive disease, carriers of one variant that leads to a complete loss of function of the gene or gene product (null or amorphic variants) remain unaffected, whereas bi-allelic null variants lead to the disease phenotype. Hypomorphic variants reduce the function of a gene or protein only partly, to a level where homozygous carriers of the hypomorphic variant do not develop a severe disease phenotype, or no discernible phenotype at all (partial loss-of-function variants). However, individuals who have inherited a hypomorphic variant and a null variant on the other allele of the same gene (compound heterozygosity) will develop disease which may be somewhat milder (Fig. 1). Hypomorphic variants have been described as the cause of other human diseases, including various collagenoses, Fanconi anemia, congenital scoliosis and retinal disease [
      • Charbel Issa P.
      • Tysoe C.
      • Caswell R.
      Late-onset pseudoxanthoma elasticum associated with a hypomorphic ABCC6 variant.
      ,
      • Fiesco-Roa M.O.
      • Giri N.
      • McReynolds L.J.
      • Best A.F.
      • Alter B.P.
      Genotype-phenotype associations in Fanconi anemia: a literature review.
      ,
      • Girisha K.M.
      • Bhavani G.S.
      • Shah H.
      • Moirangthem A.
      • Shukla A.
      • Kim O.H.
      • Nishimura G.
      • Mortier G.R.
      Biallelic variants p.Arg1133Cys and p.Arg1379Cys in COL2A1: further delineation of phenotypic spectrum of recessive Type 2 collagenopathies.
      ,
      • Moosa S.
      • Yamamoto G.L.
      • Garbes L.
      • Keupp K.
      • Beleza-Meireles A.
      • Moreno C.A.
      • Valadares E.R.
      • de Sousa S.B.
      • Maia S.
      • Saraiva J.
      • Honjo R.S.
      • Kim C.A.
      • Cabral de Menezes H.
      • Lausch E.
      • Lorini P.V.
      • Lamounier Jr., A.
      • Carniero T.C.B.
      • Giunta C.
      • Rohrbach M.
      • Janner M.
      • Semler O.
      • Beleggia F.
      • Li Y.
      • Yigit G.
      • Reintjes N.
      • Altmuller J.
      • Nurnberg P.
      • Cavalcanti D.P.
      • Zabel B.
      • Warman M.L.
      • Bertola D.R.
      • Wollnik B.
      • Netzer C.
      Autosomal-recessive mutations in MESD cause osteogenesis imperfecta.
      ,
      • Savige J.
      • Storey H.
      • Watson E.
      • Hertz J.M.
      • Deltas C.
      • Renieri A.
      • Mari F.
      • Hilbert P.
      • Plevova P.
      • Byers P.
      • Cerkauskaite A.
      • Gregory M.
      • Cerkauskiene R.
      • Ljubanovic D.G.
      • Becherucci F.
      • Errichiello C.
      • Massella L.
      • Aiello V.
      • Lennon R.
      • Hopkinson L.
      • Koziell A.
      • Lungu A.
      • Rothe H.M.
      • Hoefele J.
      • Zacchia M.
      • Martic T.N.
      • Gupta A.
      • van Eerde A.
      • Gear S.
      • Landini S.
      • Palazzo V.
      • Al-Rabadi L.
      • Claes K.
      • Corveleyn A.
      • Van Hoof E.
      • van Geel M.
      • Williams M.
      • Ashton E.
      • Belge H.
      • Ars E.
      • Bierzynska A.
      • Gangemi C.
      • Lipska-Zietkiewicz B.S.
      Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria.
      ,
      • Zernant J.
      • Lee W.
      • Collison F.T.
      • Fishman G.A.
      • Sergeev Y.V.
      • Schuerch K.
      • Sparrow J.R.
      • Tsang S.H.
      • Allikmets R.
      Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration.
      ]. Descriptions include clear genotype-phenotype correlations where hypomorphic variants lead to a milder or later-onset disease [
      • Charbel Issa P.
      • Tysoe C.
      • Caswell R.
      Late-onset pseudoxanthoma elasticum associated with a hypomorphic ABCC6 variant.
      ,
      • Fiesco-Roa M.O.
      • Giri N.
      • McReynolds L.J.
      • Best A.F.
      • Alter B.P.
      Genotype-phenotype associations in Fanconi anemia: a literature review.
      ,
      • Savige J.
      • Storey H.
      • Watson E.
      • Hertz J.M.
      • Deltas C.
      • Renieri A.
      • Mari F.
      • Hilbert P.
      • Plevova P.
      • Byers P.
      • Cerkauskaite A.
      • Gregory M.
      • Cerkauskiene R.
      • Ljubanovic D.G.
      • Becherucci F.
      • Errichiello C.
      • Massella L.
      • Aiello V.
      • Lennon R.
      • Hopkinson L.
      • Koziell A.
      • Lungu A.
      • Rothe H.M.
      • Hoefele J.
      • Zacchia M.
      • Martic T.N.
      • Gupta A.
      • van Eerde A.
      • Gear S.
      • Landini S.
      • Palazzo V.
      • Al-Rabadi L.
      • Claes K.
      • Corveleyn A.
      • Van Hoof E.
      • van Geel M.
      • Williams M.
      • Ashton E.
      • Belge H.
      • Ars E.
      • Bierzynska A.
      • Gangemi C.
      • Lipska-Zietkiewicz B.S.
      Consensus statement on standards and guidelines for the molecular diagnostics of Alport syndrome: refining the ACMG criteria.
      ] than amorphic variants.
      Fig. 1
      Fig. 1Amorphic versus hypomorphic genetic variants in recessive disease. Schematic representation of a family with two parents and one child. A: In classical autosomal recessive disease, individuals are affected who have inherited genetic variants that lead to a complete loss of function in both alleles. Such amorphic genetic variants are relatively rare in the population, and their combined frequency in compound heterozygous or homozygous genotypes corresponds to the disease's incidence in the population. B: A combination of a hypomorphic and an amorphic variant. Carriers of such a genotype have milder disease. C: Bi-allelic carriers of hypomorphic variants do not develop disease because of sufficient residual function of the gene product. This means that hypomorphic variants can be relatively common in a population; they will cause disease only in individuals who also have inherited an amorphic variant on the second allele.
      As hypomorphic variants both in heterozygous and in homozygous genotypes – in the absence of additional, more severe variants – do not cause a severe phenotype, they may be relatively common in the population [
      • Zernant J.
      • Lee W.
      • Collison F.T.
      • Fishman G.A.
      • Sergeev Y.V.
      • Schuerch K.
      • Sparrow J.R.
      • Tsang S.H.
      • Allikmets R.
      Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration.
      ]. Škorvánek et al. observed that this is the case for the p.(Trp13Gly) variant. In the extensive gnomAD database, 0.33% of alleles from all populations had this particular variant, and in the non-Finnish European population subgroup, to which most of the reported patients belong, it was even found in 590 of 128,958 alleles (0.46%). The problem with regard to clinical diagnostics is that a variant with such a relatively high frequency is considered too common to be a cause for an excessively rare disease, and the commonly applied American College of Medical Genetics and Genomics guidelines state that a population frequency ”greater than expected for the disorder” provides strong evidence that the variant is not pathogenic [
      • Richards S.
      • Aziz N.
      • Bale S.
      • Bick D.
      • Das S.
      • Gastier-Foster J.
      • Grody W.W.
      • Hegde M.
      • Lyon E.
      • Spector E.
      • Voelkerding K.
      • Rehm H.L.
      • Committee A.L.Q.A.
      Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of medical genetics and Genomics and the association for molecular pathology.
      ]. In the entire gnomAD database with data on more than 140,000 individuals, 6 persons were homozygous carriers of the p.(Trp13Gly) variant. Most algorithms used in clinical diagnostic practice would routinely filter out variants that are reported in homozygous state in several individuals in databases, with the assumption that individuals in databases are not affected by rare, severe neurological disorders.
      We cannot know a priori which variants are hypomorphic but disease causing, unless careful studies such as the one by Škorvánek et al. compile a number of patients with the hypomorphic variant in combination with additional variants and functional evidence is provided. Škorvánek et al.’s work elegantly shows that rare/very rare/extremely rare genetic variants are not the only conceivable causes for very rare Mendelian diseases. Commoner variants play a role, too, but are - somewhat paradoxically - harder to find.

      Acknowledgements

      We thank the patient described here, and her family, for their participation in our research study. The patient was examined within a research study approved by the ethics review board and with parents' informed consent. Parents provided written and informed consent. Research was funded by Region Skåne , Skåne University Hospital , Multipark – a strategic research environment at Lund University , and the Swedish government through ALF grants, all in Sweden.

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