GRID2 and Spinocerebellar Ataxia

Missense variants as a possible cause of GRID2-related spinocerebellar ataxia type 18 M. Calvo1, D. Trujillano1, N. Nahavandi1, A. Rolfs1,2, M. Tarnopolsky3, R. Abou Jamra1 1Centogene AG, Rostock, Germany 2Albrecht-Kossel-Institute for Neuroregeneration, Medical University Rostock, Rostock, Germany 3Department of Pediatrics, McMaster University, Hamilton, ON, Canada Summary Whole Exome Sequencing (WES) revealed in a Canadian patient with early-onset episodic ataxia, developmental delay, and further symptoms, two in trans missense variants in the GRID2 gene: c.2128C>T (Arg170Trp) and c.2218G>A (p.Val740Ile). GRID2 has been recently associated with spinocerebellar ataxia type 18. Based on the recent literature, our results suggest that at least one of the variants detected, c.2128C>T (Arg170Trp), could be associated with the patient´s phenotype due to its low frequency and its location in a conserved amino acid position. Clinical information • Female patient of Canadian origin • Since the age of 8 months the patient showed episodic ataxia, failure to thrive, developmental delay, dystonic posturing and seizures. • At the age of 12 years, the patient shows in addition progressive cerebellar atrophy and nystagmus. WES Technology at Centogene: CentoXome® raw reads • Full list of variants 60K 73479 variants in this case • Exonic and splice 13K plicons 293.903 Analysis statistics ~3K • Non-synonymous and splicing Number of mapped reads 39.327.751 Percent reads on target 95,35% • Only rare variants (MAF<1%) Average reads per amplicon150 127,6 with at leastNumber of amplicons 20 reads293.903 Average reads per amplicon 127,6 8 • Only segregating Amplicons with at least 20 reads 93,66% • Top based on MAF and in silico93,66% parameters 2 GRID2 gene 1 • Top based on function of gene and literature GRID2 and spinocerebellar ataxia • GRID2 (chromosome 4q22) encodes a glutamate receptor that is thought to be selectively expressed in the Purkinje cells of the cerebellum. • It has been recently associated with autosomal recessive spinocerebellar ataxia type 18 in humans (SCAR18, OMIM: 616204), which is characterized by early onset severe cerebellar ataxia, ocular movement abnormalities, and intellectual disability with progressive cerebellar atrophy. 0 • Homozygous or compound heterozygous large deletions encompassing single or several exons of GRID2 have been described as disease-causing in three families, mimicking the hotfoot mouse phenotype. The first de novo missense mutations in humans, resulting in progressive cerebellar ataxia in adults and congenital ataxia in children, have been very recently described and are located at the same (or a nearby) amino acid position as the one in the lurcher mouse (which affects Ala654). Variants identified in GRID2 in the index patient and segregation in the parents In silico predictions Disease Inherited/ Conservation (according to Inheritance Zygosity c-position p-position Significance Frequency (ExAC) Acquired (nucleotide/ amino OMIM) Damaging/benign acid/physicochemical difference Variant of Polyphen-2, SIFT, Inherited uncertain Not MutationTaster – probably Autosomal Heterozygous c.2128C>T p.Arg710Trp from 0.00005 clinical conserved/high/moderate damaging recessive mother Autosomal significance AlignGVGD - toleration spinocerebellar recessive Variant of 0.001 SIFT, MutationTaster – ataxia type18 Inherited uncertain (detected in a probably damaging (OMIM: 616204) Heterozygous c.2218G>A p.Val740Ile High/high/small from father clinical homozygous state in Polyphen-2, AlignGVGD- significance two cases) toleration Arg710 1007 1 Ala654 Val740 The variants detected in the index patient are located in trans. Further testing is needed M3 M4 M1 S2 GRID2 in order to determine whether both variants are involved in the patient´s phenotype. S1 Large deletions/duplications were excluded by qPCR analysis S1, S2: extracellular ligand binding subdomains M3S2-linker M1, M3, M4: transmembrane domains responsible for the pore formation Mutations in Ala654 cause the lurcher ataxia Adapted from Coutelier et al., 2015 – PMID: 25907855 phenotype in mouse and human Conclusion We see most symptoms of the patient clearly overlapping with those previously described in the families with GRID2-related SCA. Although further characterization is needed, our results initially suggest that missense variants other than those affecting the amino acid mutation in the lurcher mouse, might be disease-causing for SCA with a comparable phenotype. Due to its low frequency and its location in a highly 0 conserved amino acid position, we consider the c.2128C>T to be a better candidate. Variant c.2218G>A has been previously detected in a homozygous state according to ExAC; however, as it is in trans with c.2128C>T and GRID2-related SCA may be inherited in an autosomal recessive manner, we assume a possible contribution of this variant to the patient’s phenotype. References Lalouette et al., Genomics. 1998 May 15;50:9-13 Utine et al., J Child Neurol. 2013 Jul;28:926-32 Takayama et al.,Neurosci Lett. 1995 Mar 24;188:89-92 Lalonde et al., Physiol Behav. 2003 Nov;80:333-9 Van Schil et al., Genet Med. 2015 Apr;17:291-9 Hills et al., Neurology. 2013 Oct 15;81:1378-86 Coutelier et al., Neurology. 2015 Apr 28;84:1751-9. Hu et al., Genomics. 1998 Jan 1;47:143-5 Disclosure of conflict of interest: Contact details: [email protected] This study was sustained in part by Centogene AG, Rostock, Germany Author of the presentation, María Calvo, and 3 co-authors are employees of Centogene AG, Rostock,Germany www.centogene.com .

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