New HSP genotypes and phenotypes - HSP Research Foundation

Research from Belgium, France, USA, Germany, Turkey, Serbia, Spain, Italy, China, Poland, Netherlands, Japan, Cyprus, Finland, Austria, Lebanon, Chile, Morocco

What are genotypes and phenotypes?

The distinction between genotype and phenotype is the difference between someone’s heredity, the set of genes they carry, i.e. their genotype and what that set of genes produces, i.e. their physical and other characteristics or phenotype.

Physical characteristics (phenotype) are determined by the set of genes (genotype) someone has.

Physical characteristics include appearance, development and behaviour. Examples include height; eye, skin and hair color; body shape and size. Phenotype also includes characteristics that can be observed or measured such as levels of hormones, blood type and behaviour.

Phenotype is determined as well as by environmental influences on the genes. Identical twins, who have identical genotypes, eventually develop some differences because each twin will encounter different environmental influences as they develop and age.

SPTAN1 a candidate gene for spastic paraplegia

A substantial international collaboration found 5 new variants in 22 people in the SPTAN1 gene associated with cerebellar ataxia, spastic paraplegia and spastic ataxia.

Background: Pathogenic variants in SPTAN1 have been linked to a remarkably broad phenotypical spectrum. Clinical presentations include epileptic syndromes, intellectual disability, and hereditary motor neuropathy.

Objectives: We investigated the role of SPTAN1 variants in rare neurological disorders such as ataxia and spastic paraplegia.

Methods: We screened 10,000 NGS datasets across two international consortia and one local database, indicative of the level of international collaboration currently required to identify genes causative for rare disease. We performed in silico modeling of the identified SPTAN1 variants.

Results: We describe 22 patients from 14 families with five novel SPTAN1 variants. Of six patients with cerebellar ataxia, four carry a de novo SPTAN1 variant and two show a sporadic inheritance. In this group, one variant (p.Lys2083del) is recurrent in four patients. Two patients have novel de novo missense mutations (p.Arg1098Cys, p.Arg1624Cys) associated with cerebellar ataxia, in one patient accompanied by intellectual disability and epilepsy. We furthermore report a recurrent missense mutation (p.Arg19Trp) in 15 patients with spastic paraplegia from seven families with a dominant inheritance pattern in four and a de novo origin in one case. One further patient carrying a de novo missense mutation (p.Gln2205Pro) has a complex spastic ataxic phenotype. Through protein modeling we show that mutated amino acids are located at crucial interlinking positions, interconnecting the three-helix bundle of a spectrin repeat.

Conclusions: We show that SPTAN1 is a relevant candidate gene for ataxia and spastic paraplegia. We suggest that for the mutations identified in this study, disruption of the interlinking of spectrin helices could be a key feature of the pathomechanism. © 2022 International Parkinson and Movement Disorder Society.

De Novo and Dominantly Inherited SPTAN1 Mutations Cause Spastic Paraplegia and Cerebellar Ataxia

Liedewei Van de Vondel 1 2 , Jonathan De Winter 1 2 3 , Danique Beijer 1 2 4 , Giulia Coarelli 5 , Melanie Wayand 6 7 , Robin Palvadeau 8 , Martje G Pauly 9 10 , Katrin Klein 11 , Maren Rautenberg 11 , Léna Guillot-Noël 5 , Tine Deconinck 12 , Atay Vural 13 , Sibel Ertan 13 , Okan Dogu 14 , Hilmi Uysal 15 , Vesna Brankovic 16 , Rebecca Herzog 9 , Alexis Brice 5 , Alexandra Durr 5 , Stephan Klebe 17 , Friedrich Stock 18 , Almut Turid Bischoff 19 , Tim W Rattay 6 7 , María-Jesús Sobrido 20 21 , Giovanna De Michele 22 , Peter De Jonghe 2 3 , Thomas Klopstock 19 23 24 , Katja Lohmann 10 , Ginevra Zanni 25 , Filippo M Santorelli 26 , Vincent Timmerman 2 27 , Tobias B Haack 11 28 , Stephan Züchner 4 , PREPARE Consortium; Rebecca Schüle 6 7 , Giovanni Stevanin 5 29 , Matthis Synofzik 6 7 , A Nazli Basak 8 , Jonathan Baets 1 2 3

1. Translational Neurosciences, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.

2. Laboratory of Neuromuscular Pathology, Institute Born-Bunge, University of Antwerp, Antwerp, Belgium.

3. Neuromuscular Reference Centre, Department of Neurology, Antwerp University Hospital, Antwerp, Belgium.

4. Dr John T. Macdonald Foundation Department of Human Genetics, John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, USA.

5. Sorbonne University, ICM-Paris Brain Institute, INSERM, CNRS, APHP, Pitié Salpêtrière Hospital, Paris, France.

6. Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research (HIH), Center of Neurology, University of Tübingen, Tübingen, Germany.

7. German Center for Neurodegenerative Diseases (DZNE), University of Tübingen, Tübingen, Germany.

8. Koc University, School of Medicine, Suna and Inan Kirac Foundation, Istanbul, Turkey.

9. Department of Neurology, University Hospital Schleswig Holstein, Lübeck, Germany.

10. Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.

11. Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany.

12. Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Edegem, Belgium.

13. School of Medicine, Department of Neurology, Koc University, Istanbul, Turkey.

14. Department of Neurology, School of Medicine, Mersin University, Mersin, Turkey.

15. Department of Neurology, School of Medicine, Akdeniz University, Antalya, Turkey.

16. Clinic for Child Neurology and Psychiatry, University of Belgrade, Belgrade, Serbia.

17. Department of Neurology, University Hospital Essen, Essen, Germany.

18. Institute of Human Genetics, University Hospital Essen, Essen, Germany.

19. Department of Neurology, Friedrich-Baur-Institute, LMU Munich, Munich, Germany.

20. Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Santiago de Compostela, Spain.

21. Neurogenetics Research Group, Instituto de Investigación Sanitaria (IDIS), Hospital Clínico Universitario, SERGAS, Santiago de Compostela, Spain.

22. Department of Neurosciences and Reproductive and Odontostomatological Sciences, Federico II University, Naples, Italy.

23. German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.

24. Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.

25. Unit of Neuromuscular and Neurodegenerative Disorders, Department of Neurosciences, Bambino Gesù Children’s Hospital, Rome, Italy.

26. Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy.

27. Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.

28. Centre for Rare Diseases, University of Tübingen, Tübingen, Germany.

29. Paris Sciences Lettres Research University, Ecole Pratique des Hautes Etudes, Paris, France.

SPG5 impairments described

Imaging and biochemical indicators show that breakdown and loss of the nerve sheath (demyelination) and axonal dieback lead to a loss of integrity in brain white matter, however grey matter is seemingly unaffected.

Background and purpose: In spastic paraplegia type 5, spinal cord atrophy and white matter signal abnormalities in the brain are the main MR imaging alterations. However, the specific mechanism remains unclear. We explored the microstructural changes occurring in spastic paraplegia type 5 and assessed the relation between MR imaging and clinical data.

Materials and methods: Seventeen patients with spastic paraplegia type 5 and 17 healthy controls were scanned with DTI and T1 mapping on a 3T MR imaging scanner. Fractional anisotropy, mean diffusivity, radial diffusivity, axial diffusivity, and T1 values were obtained using Tract-Based Spatial Statistics and the Spinal Cord Toolbox. Neurofilament light and myelin basic protein in the CSF were measured. The differences in MR imaging and biochemical data between patients with spastic paraplegia type 5 and healthy controls were compared using the Student t test.

Results: A widespread reduction of fractional anisotropy values and an elevation of mean diffusivity, T1, and radial diffusivity values were found in most cervical, T4, and T5 spinal cords; corona radiata; optic radiations; and internal capsules in spastic paraplegia type 5. A variation in axial diffusivity values was shown only in C2, C6, and the corona radiata but not in the gray matter. The levels of neurofilament light and myelin basic protein were higher in those with spastic paraplegia type 5 than in healthy controls (myelin basic protein, 3507 [SD, 2291] versus 127 [SD, 219] pg/mL; neurofilament light, 617 [SD, 207] versus 265 [SD, 187] pg/mL; P < .001). No correlation was found between the clinical data and MR imaging-derived measures.

Conclusions: Multiparametric MR imaging and biochemical indicators demonstrated that demyelination (mainly) and axonal loss led to the white matter integrity loss without gray matter injury in spastic paraplegia type 5.

White Matter Alterations in Spastic Paraplegia Type 5: A Multiparametric Structural MRI Study and Correlations with Biochemical Measurements

Y Liu 1 2 , Z Ye 3 4 , J Hu 1 , Z Xiao 5 , F Zhang 1 , X Yang 1 , W Chen 3 4 6 , Y Fu 3 4 , D Cao 7 8

1. From the Departments of Radiology (Y.L., J.H., F.Z., X.Y., D.C.).

2. Department of Medical Imaging Technology (Y.L.), College of Medical Technology and Engineering.

3. Neurology and Institute of Neurology (Z.Y., W.C., Y.F.).

4. Department of Neurology and Institute of Neurology (Z.Y., W.C., Y.F.).

5. Department of Biomedical Sciences (Z.X.), University of Pennsylvania, Philadelphia, Pennsylvania.

6. Fujian Key Laboratory of Molecular Neurology (W.C.), Fujian Medical University, Fuzhou, China.

7. From the Departments of Radiology (Y.L., J.H., F.Z., X.Y., D.C.)

8. Key Laboratory of Radiation Biology of Fujian Higher Education Institutions (D.C.), First Affiliated Hospital, Fujian Medical University, Fuzhou, China.

5 new ATP1A1 variants identified in 5 sporadic cases of severe, complex spastic paraplegia in unrelated children

Abstract

ATP1A1 encodes the α1 subunit of the sodium-potassium ATPase, an electrogenic cation pump highly expressed in the nervous system. Pathogenic variants in other subunits of the same ATPase, encoded by ATP1A2 or ATP1A3, are associated with syndromes like hemiplegic migraine, dystonia, or cerebellar ataxia. Worldwide, only sixteen families have been reported carrying pathogenic ATP1A1 variants to date. Associated phenotypes are axonal neuropathies, spastic paraplegia, and hypomagnesemia with seizures and intellectual disability.

By whole exome or genome sequencing, we identified five novel heterozygous ATP1A1 variants, c.674A>G;p.Gln225Arg, c.1003G>T;p.Gly335Cys, c.1526G>A;p.Gly509Asp, c.2152G>A;p.Gly718Ser, and c.2768T>A;p.Phe923Tyr in five unrelated children with intellectual disability, spasticity, and peripheral, motor predominant neuropathy. Additional features were sensory loss, sleep disturbances, and seizures. All variants occurred de novo and are absent from control populations (MAF GnomAD=0). Affecting conserved amino acid residues and constrained regions, all variants have high pathogenicity in-silico prediction scores. In HEK cells transfected with ouabain-insensitive ATP1A1 constructs, cell viability was significantly decreased in mutants after 72h treatment with the ATPase inhibitor ouabain, demonstrating loss of ATPase function. Replicating the haploinsufficiency mechanism of disease with a gene-specific assay provides pathogenicity information and increases certainty in variant interpretation. This study further expands the genotype-phenotype spectrum of ATP1A1.

SOURCE: Neurology. 2022 Feb 2; 10.1212/WNL.0000000000013276. doi: 10.1212/WNL.0000000000013276. Online ahead of print. PMID: 35110381 Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the American Academy of Neurology.

De Novo ATP1A1 Variants in an Early-Onset Complex Neurodevelopmental Syndrome

Maike F Dohrn 1 2 , Adriana P Rebelo 1 , Siddharth Srivastava 3 , Gerarda Cappuccio 4 5 , Robert Smigiel 6 , Alka Malhotra 7 , Donald Basel 8 , Ingrid van de Laar 9 , Rinze Frederik Neuteboom 10 , Coranne Aarts-Tesselaar 11 , Sonal Mahida 3 , Nicola Brunetti-Pierri 4 5 , Ryan Taft 7 , Stephan Züchner 12

1. Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA.

2. Department of Neurology, RWTH Aachen University Hospital, Aachen, Germany.

3. Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA.

4. Department of Translational Medicine, Federico II University, Naples, Italy.

5. Telethon Institute of Genetics and Medicine, Pozzuoli, Naples, Italy.

6. Department of Pediatrics and Rare Disorders, Wroclaw Medical University, Wroclaw, Poland.

7. Illumina Inc, San Diego, CA. USA.

8. Division of Pediatric Genetics, Department of Genetics, Medical College of Wisconsin, Milwaukee, WI, USA.

9. Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.

10. Department of Neurology, Eramus MC, Medical Center Rotterdam, The Netherlands.

11. Amphia Hospital, Breda, the Netherlands.

12. Dr. John T. Macdonald Foundation, Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA

SPG31 investigated in large study

25 individuals from 15 families were identified as having SPG31 in this large study in Japan, including three asymptomatic carriers, all of whom were female. Of the 14 different genetic variants found, 11 were new.

70% showed a pure form of HSP with the remainder having complicated HSP with peripheral neuropathy. 50% had symptoms before the age of 10 with 20% at age 41 – 50.

The study was possible only because of the availability of DNA samples in a large biobank of the Japan Spastic Paraplegia Research Consortium (JASPAC) who have done excellent work to advance global knowledge and understanding of the HSPs over many years.

Abstract

SPG31 is an autosomal dominant hereditary spastic paraplegia caused by pathogenic variants in the receptor expression-enhancing protein 1 (REEP1) gene.

We analyzed 488 DNA samples from unrelated HSP patients collected by Japan Spastic Paraplegia Research Consortium and found 15 Japanese SPG31 families. We investigated each family and found a total of 25 individuals with REEP1 variants (comprising 22 patients and three asymptomatic carriers). Fourteen REEP1 variants (five missense, three nonsense, four frameshift, one splice site, and one large deletion) including 11 novel ones were detected.

70% of the patients (14 of 20) showed a pure form and the others (6 of 20) showed a complicated form with peripheral neuropathy. 50% had neurological symptoms before the age of 10 and 20% of them at age 41-50. The mean age of onset was 19.6 ± 18.7 (from 5 to 67, n = 15) years for males and 32.8 ± 24.7 (from 4 to 60, n = 5) years for females. Although the difference was not statistically significant (p = 0.38, Mann-Whitney U test), males tended to have an earlier age of onset. Moreover, all three asymptomatic carriers were female.

We investigated additional factors as to phenotypic appearance in one family with apparent intrafamilial variability in age at onset and clinical severity, but no additional factors including gene variants could be found.

This is the first report of clinical and genetic findings of SPG31 in Japan, which may lead to further studies of the genotype-phenotype correlation of SPG31.

A clinical and genetic study of SPG31 in Japan

Takanori Hata 1 , Haitian Nan 1 , Kishin Koh 1 , Hiroyuki Ishiura 2 , Shoji Tsuji 3 4 , Yoshihisa Takiyama 5

1. Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898, Japan.

2. Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.

3. Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan.

4. Department of Neurology, International University of Health and Welfare, Chiba, 286-8686, Japan.

5. Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, 409-3898, Japan.

Huge study of 1550 people with HSP

Genetic analysis using a targeted sequencing panel found a causative variant in 31% of cases, covering 35 of the 65 genes screened. SPAST/SPG4 and SPG7 represented 9% and 5% of the whole population. 382 different causative variants, 30 of them structural, were identified. The approach allows detection of structural variants more efficiently than in exome datasets. This is important as structural variants represent a significant proportion (~6%) of the HSPs, notably for SPAST/SPG4 and REEP1/SPG31.

Abstract

Hereditary spastic paraplegia refers to rare genetic neurodevelopmental and/or neurodegenerative disorders in which spasticity due to length-dependent damage to the upper motor neuron is a core sign. Their high clinical and genetic heterogeneity makes their diagnosis challenging. Multigene panels allow a high-throughput targeted analysis of the increasing number of genes involved using next-generation sequencing.

We report here the clinical and genetic results of 1550 index cases tested for variants in a panel of hereditary spastic paraplegia related genes analyzed in routine diagnosis. A causative variant was found in 475 patients (30.7%) in 35/65 screened genes. SPAST and SPG7 were the most frequently mutated genes, representing 142 (9.2%) and 75 (4.8%) index cases of the whole series, respectively. KIF1A, ATL1, SPG11, KIF5A and REEP1 represented more than 1% (> 17 cases) each. There were 661 causative variants (382 different ones) and 30 of them were structural variants.

This large cohort allowed us obtaining an overview of the clinical and genetic spectrum of hereditary spastic paraplegia in clinical practice. Because of the wide phenotypic variability, there was no very specific sign that could predict the causative gene but there were some constellations of symptoms that were found often related to specific subtypes. Finally, we confirmed the diagnostic effectiveness of a targeted sequencing panel as a first-line genetic test in hereditary spastic paraplegia. This is a pertinent strategy because of the relative frequency of several known genes (i.e.: SPAST, KIF1A) and it allows identifying variants in the rarest involved genes and to detect structural rearrangements via coverage analysis, which is less efficient in exome data sets. It is crucial because these structural variants represent a significant proportion of the pathogenic hereditary spastic paraplegia variants (∼6% of patients), notably for SPAST and REEP1.

In a subset of 42 index cases negative for the targeted multigene panel, subsequent whole exome sequencing allowed to reach a theoretical diagnosis yield of ∼50%. We then propose a two-step strategy combining the use of a panel of genes followed by whole exome sequencing in negative cases.

SOURCE: Brain. 2022 Jan 4;awab386. doi: 10.1093/brain/awab386. Online ahead of print. PMID: 34983064 © The Author(s) (2022). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved.

Clinical and genetic spectra of 1550 index patients with hereditary spastic paraplegia

Jean-Loup Méreaux 1 2 3 , Guillaume Banneau 4 5 , Mélanie Papin 1 2 , Giulia Coarelli 1 4 , Rémi Valter 1 2 , Laure Raymond 1 2 , Bophara Kol 4 , Olivier Ariste 6 , Livia Parodi 1 2 7 , Laurène Tissier 4 , Mathilde Mairey 1 2 , Samia Ait Said 4 , Celia Gautier 1 2 , Marine Guillaud-Bataille 4 , French SPATAX clinical network; Sylvie Forlani 1 , Pierre de la Grange 6 , Alexis Brice 1 , Giovanni Vazza 7 , Alexandra Durr 1 4 , Eric Leguern 1 4 , Giovanni Stevanin 1 2 4

French SPATAX clinical network: Mathieu Anheim, Jean-Philippe Azulay, Odile Boesfplug-Tanguy, Perrine Charles, Alexandra Durr, Cyril Goizet, Didier Hannequin, Vincent Huin, Michel Koenig, Pierre Labauge, Eric Leguern, Karine N’Guyen, Mathilde Renaud, Diana Rodriguez, Christophe Verny

1. Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, APHP, Hôpital de la Pitié Salpêtrière, 75013 Paris, France.

2. 3Paris Sciences Lettres University, EPHE, 75000 Paris, France.

3. Rouen University Hospital, 76000 Rouen, France.

4. APHP, Sorbonne Université, Department of Medical Genetics, 75013 Paris, France.

5. Département de Génétique Médicale, Institut Fédératif de Biologie, Hôpital Purpan, 31000 Toulouse, France.

6. GenoDiag-GenoSplice, Paris Biotech Santé, 75014 Paris, France.

7. Department of Biology, University of Padua, 35100 Padua, Italy.

Two new heterozygous variants detected in the TECPR2 gene (SPG49)

Here is a case of a child with normal mental development and good athletic ability up to 10 years old, presenting with unstable temperature, cognitive impairment, spastic ataxia, and paroxysmal convulsions, suggesting differences in the clinical phenotype of SPG49 in different ethnicities.

Background: Hereditary spastic paraplegia 49 (HSP49) is an autosomal recessive genetic disease first discovered in 2012; and which the mutation primarily affects Bukharian Jewish patients.

Case presentation: The present case reports the first instance of HSP49 detected in China. The patient had normal mental development and good athletic ability before 10 years old and presented with unstable temperature, cognitive impairment, spastic ataxia, and paroxysmal convulsions.

Genetic diagnosis was based on detection of whole exons and two heterozygous variants in the exon region of the TECPR2 gene: c.1729C > T and c.4189G > A. Mutations at these two sites have not been previously reported.

Conclusions: This case expands the gene mutation spectrum and clinical phenotypic characteristics of autosomal recessive HSP in China; moreover, it indicates differences in the clinical phenotype of HSP49 in different ethnicities. In addition, this reported provides further evidence regarding the effectiveness of targeted next-generation sequencing technology in improving the efficiency and diagnostic rate of genetic diagnosis of HSP.

Novel detection of mutation in the TECPR2 gene in a Chinese hereditary spastic paraplegia 49 patient: a case report

Yalin Guan 1 2 , Hui Lu 3 4 , Wenchao Zuo 3 4 , Xiaodan Wang 3 4 , Shimin Wang 3 4 , Xinping Wang 3 4 , Feng Liu 3 4 , Kun Jia 3 4 , Rui Gao 3 4 , Hao Wu 3 4 , Zhihong Shi 3 4 , Yong Ji 3 4

1. Department of Neurology, Tianjin Huanhu Hospital, Tianjin, 300350, China.

2. Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Disease, Tianjin, 300350, China.

3. Department of Neurology, Tianjin Huanhu Hospital, Tianjin, 300350, China.

4. Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Disease, Tianjin, 300350, China.

New SPG7 variant found

A case of SPG7 has been reported for the first time in Cyprus. Five affected individuals from the one family were found to have an autosomal recessive spastic ataxia.

Abstract

The SPG7 gene encodes the paraplegin protein, an inner mitochondrial membrane-localized protease. It was initially linked to pure and complicated hereditary spastic paraplegia with cerebellar atrophy, and now represents a frequent cause of undiagnosed cerebellar ataxia and spastic ataxia.

We hereby report the molecular characterization and the clinical features of a large Cypriot family with five affected individuals presenting with spastic ataxia in an autosomal recessive transmission mode, due to a novel SPG7 homozygous missense variant. Detailed clinical histories of the patients were obtained, followed by neurological and neurophysiological examinations. Whole exome sequencing (WES) of the proband, in silico gene panel analysis, variant filtering and family segregation analysis of the candidate variants with Sanger sequencing were performed. RNA and protein expression as well as in vitro protein localization studies and mitochondria morphology evaluation were carried out towards functional characterization of the identified variant.

The patients presented with typical spastic ataxia features while some intrafamilial phenotypic variation was noted. WES analysis revealed a novel homozygous missense variant in the SPG7 gene (c.1763C > T, p. Thr588Met), characterized as pathogenic by more than 20 in silico prediction tools. Functional studies showed that the variant does not affect neither the RNA or protein expression, nor the protein localization. However, aberrant mitochondrial morphology has been observed thus indicating mitochondrial dysfunction and further demonstrating the pathogenicity of the identified variant.

Our study is the first report of an SPG7 pathogenic variant in the Cypriot population and broadens the spectrum of SPG7 pathogenic variants.

SOURCE: Front Genet. 2022 Jan 13;12:812640. doi: 10.3389/fgene.2021.812640. eCollection 2021. PMID: 35096021 Copyright © 2022 Votsi, Ververis, Nicolaou, Christou, Christodoulou and Zamba-Papanicolaou.

A Novel SPG7 Gene Pathogenic Variant in a Cypriot Family With Autosomal Recessive Spastic Ataxia

Christina Votsi 1 , Antonis Ververis 1 , Paschalis Nicolaou 1 , Yiolanda-Panayiota Christou 2 , Kyproula Christodoulou 1 , Eleni Zamba-Papanicolaou 3

1. Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.

2. Neurobiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.

3. Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.

New variant in SPG11 identified

Two siblings in a consanguinous family showed a similar pattern of gait disturbance due to spastic paraplegia from childhood and progressive cognitive decline from early adulthood.

Abstract

Individuals with hereditary spastic paraplegia (HSP) are known to present with a variety of symptoms, including intellectual disability, cognitive decline, parkinsonism, and epilepsy. We report here our experience of treating a family with consanguinity, including three patients with HSP-related symptoms.

We performed whole-exome sequencing and identified a novel pathogenic nonsense variant, c.4544G > A, p.W1515*, in the SPG11 gene. Proband and her affected sister showed the same course of gait disturbance due to spastic paraplegia from childhood and progressive cognitive decline from early adulthood. Brain MRI depicted a thinning of the corpus callosum, severe atrophic changes in the frontotemporal lobes, and ears of the lynx sign. Patients with SPG11 variants clinically present with distinctive symptoms.

A complex form of hereditary spastic paraplegia harboring a novel variant, p.W1515*, in the SPG11 gene

Kensuke Daida 1 , Yosuke Nishioka 2 , Yuanzhe Li 1 , Hiroyo Yoshino 3 , Manabu Funayama 1 3 , Nobutaka Hattori 1 3 , Kenya Nishioka 1

1. Department of Neurology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.

2. Nishioka Memorial Central Clinic, 375 Hasama, Isobecho, Shima-shi, Mie 517-0214, Japan.

3. Research Institute for Diseases of Old Age, Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.

New variant identified in ATL1 gene

Causes complex, early-onset spastic quadriplegia. Tests indicate a gain-of-function disease mechanism uncommon for the ATL1 gene.

Abstract

Hereditary spastic paraplegia (HSP) comprises a heterogeneous group of neuropathies affecting upper motor neurons and causing progressive gait disorder. Mutations in the gene SPG3A/atlastin-1 (ATL1), encoding a dynamin superfamily member, which utilizes the energy from GTP hydrolysis for membrane tethering and fusion to promote the formation of a highly branched, smooth endoplasmic reticulum (ER), account for approximately 10% of all HSP cases. The continued discovery and characterization of novel disease mutations are crucial for our understanding of HSP pathogenesis and potential treatments.

Here, we report a novel disease-causing, in-frame insertion in the ATL1 gene, leading to inclusion of an additional asparagine residue at position 417 (N417ins). This mutation correlates with complex, early-onset spastic quadriplegia affecting all four extremities, generalized dystonia, and a thinning of the corpus callosum. We show using limited proteolysis and FRET-based studies that this novel insertion affects a region in the protein central to intramolecular interactions and GTPase-driven conformational change, and that this insertion mutation is associated with an aberrant pre-hydrolysis state. While GTPase activity remains unaffected by the insertion, membrane tethering is increased, indicative of a gain-of-function disease mechanism uncommon for ATL1-associated pathologies.

In conclusion, our results identify a novel insertion mutation with altered membrane tethering activity that is associated with spastic quadriplegia, potentially uncovering a broad spectrum of molecular mechanisms that may affect neuronal function.

A novel insertion mutation in atlastin 1 is associated with spastic quadriplegia, increased membrane tethering, and aberrant conformational switching

Carolyn M Kelly 1 , Peter J Zeiger 2 , Vinodh Narayanan 3 , Keri Ramsey 4 , Holger Sondermann 5

1. Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.

2. Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.

3. Center for Rare Childhood Disorders, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA.

4. Center for Rare Childhood Disorders, Translational Genomics Research Institute (TGen), Phoenix, Arizona, USA.

5. Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA; CSSB Centre for Structural Systems Biology, Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; CSSB Centre for Structural Systems Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.

New SPAST variant causing pure HSP discovered

Abstract

Hereditary spastic paraplegias (HSPs) include a group of neurodegenerative disorders characterized by slowly progressive spasticity and weakness of the lower extremities, caused by axon degeneration of corticospinal tracts. Spastic paraplegia type 4 (SPG4) is the most common autosomal dominant form of HSP and is caused by mutations in the SPAST gene. SPAST gene encodes for the protein spastin, a member of the ATPases Associated with a variety of cellular Activity (AAA) family.

We describe a new variant in SPAST gene, within an Italian family affected by pure HSP. In particular, we found a heterozygous intragenic microdeletion of 3T in exon 13 of SPG4 gene. The 3T deletion results in a mutated protein with a unique leucine residues deletion at the protein position 508, in the AAA ATPase domain. This variant is not registered in any public database either as rare normal variant nor as mutation in SPAST gene and the importance of this amino acid is confirmed by the absolute conservation in multiple alignments with diverse species.

We conclude that the novel SPAST gene variant identified is probably pathogenic and destabilizes the precise arrangement of the nucleotide binding domain, with a consequent loss-of-function of the mutated spastin protein.

SOURCE: Acta Biomed. 2021 Nov 18;92(S1):e2021220. doi: 10.23750/abm.v92iS1.11608. PMID: 35132972

Amplifying the spectrum of SPAST gene mutations

Lorenzo Verriello 1 , Incoronata Renata Lonigro 2 , Maria Elena Pessa 3 , Elena Betto 4 , Giada Pauletto 5 , Federico Fogolari 6 , Gian Luigi Gigli 7 , Francesco Curcio 8

1. Neurology Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy. [email protected].

2. Institute of Clinical Pathology, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy. [email protected].

3. Azienda Ospedaliero Universitaria Friuli Centrale. [email protected].

4. Institute of Clinical Pathology, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy. [email protected].

5. Neurology Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy. [email protected].

6. Department of Mathematics, Informatics and Physics (DMIF), University of Udine, Italy. [email protected].

7. Clinical Neurology Unit, Department of Neurosciences, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy. [email protected].

8. Institute of Clinical Pathology, Santa Maria della Misericordia University Hospital, ASUFC, Udine, Italy.

New variant in the AP4B1 gene causing SPG47 identified

Another variant in the gene was also discovered and classified as being of uncertain significance.

Abstract

Pathogenic variants in the AP4B1 gene lead to a rare form of hereditary spastic paraplegia (HSP) known as SPG47.

We report on a patient with a clinical suspicion of complicated HSP of the lower limbs with intellectual disability, as well as a novel homozygous noncanonical splice site variant in the AP4B1 gene, in which the effect on splicing was validated by RNA analysis. We sequenced 152 genes associated with HSP using Next-Generation Sequencing (NGS). We isolated total RNA from peripheral blood and generated cDNA using reverse transcription-polymerase chain reaction (RT-PCR). A region of AP4B1 mRNA was amplified by PCR and the fragments obtained were purified from the agarose gel and sequenced. We found a homozygous variant of uncertain significance in the AP4B1 gene NM_006594.4: c.1511-6C>G in the proband. Two different AP4B1 mRNA fragments were obtained in the patient and his carrier parents. The shorter fragment was the predominant fragment in the patient and revealed a deletion with skipping of the AP4B1 exon 10. The patient’s longer fragment corresponded to an insertion of the last five nucleotides of AP4B1 intron 9. We confirmed that this variant affects the normal splicing of RNA, sustaining the molecular diagnosis of SPG47 in the patient.

Hereditary spastic paraplegia associated with a novel homozygous intronic noncanonical splice site variant in the AP4B1 gene

Clara Gómez-González 1 , Cristina Pizarro-Sánchez 1 , Carlos Rodríguez-Antolín 2 3 , Ignacio Pascual-Pascual 4 , Mar Garcia-Romero 4 , Carmen Rodriguez-Jiménez 5 , Rubén de Sancho-Martín 1 , Ángela Del Pozo-Mate 6 , Mario Solís-López 6 , Carmen Prior-de Castro 1 , Rosa J Torres 7 8

1. Department of Molecular Genetics, INGEMM, La Paz University Hospital, Madrid, Spain.

2. Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain.

3. Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.

4. Department of Paediatric Neurology, La Paz University Hospital, Madrid, Spain.

5. Department of Next Generation Sequencing, INGEMM, La Paz University Hospital, Madrid, Spain.

6. Department of Bioinformatics, INGEMM, La Paz University Hospital, Madrid, Spain.

7. Biochemistry Laboratory, La Paz University Hospital Health Research Institute (FIBHULP), IdiPAZ, Madrid, Spain.

8. Centre for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Spain.

Complex case of SPG6 described

23% of SPG6 cases are complex, with epilepsy the most common complicating factor (10%) followed by peripheral neuropathy (5%). It was also found that seizures might not always be drug responsive.

Abstract

SPG6, caused by NIPA1 (nonimprinted in Prader-Willi/Angelman syndrome) gene pathogenic variants, is mainly considered as a pure autosomal dominant hereditary spastic paraplegia (AD-HSP), even if descriptions of complex cases have also been reported. We detected the common c.316G > A, p.(Gly106Arg) pathogenic de novo substitution in a 10-year-old patient with HSP and drug-resistant eyelid myoclonia with absences.

In order to assess the significance of this association, we reviewed the literature to find that 25/110 (23%) SPG6 cases are complex, including a heterogeneous spectrum of comorbidities, in which epilepsy is most represented (10%), but also featuring peripheral neuropathy (5.5%), amyotrophic lateral sclerosis (3.6%), memory deficits (3.6%) or cognitive impairment (2.7%), tremor (2.7%) and dystonia (0.9%).

From this literature review and our single case experience, two main conclusions can be drawn. First, SPG6 is an AD-HSP with both pure and complex presentation, and frequent occurrence of epilepsy within the spectrum of genetic generalized epilepsies (absences, bilateral tonic-clonic, bilateral tonic-clonic with upper limbs myoclonic seizures and eyelid myoclonia with absences). Second, opposed to previous descriptions, seizures might not always be drug responsive.

SPG6 (NIPA1 variant): A report of a case with early-onset complex hereditary spastic paraplegia and brief literature review

Carlotta Spagnoli 1 , Silvia Schiavoni 2 , Susanna Rizzi 2 , Grazia Gabriella Salerno 2 , Daniele Frattini 2 , Juha Koskenvuo 3 , Carlo Fusco 4

1. Department of Pediatrics, Child Neurology Unit, Azienda USL- IRCCS di Reggio Emilia, Reggio Emilia, Italy.

2. Department of Pediatrics, Child Neurology Unit, Azienda USL- IRCCS di Reggio Emilia, Reggio Emilia, Italy.

3. Blueprint Genetics, Helsinki, Finland.

4. Department of Pediatrics, Child Neurology Unit, Azienda USL- IRCCS di Reggio Emilia, Reggio Emilia, Italy; Department of Pediatrics, Pediatric Neurophysiology Laboratory, Azienda USL- IRCCS di Reggio Emilia, Reggio Emilia, Italy.

10 new KIF1A variants found in this study of 28 cases

Most of the cases were sporadic in origin and presented features on an ataxia-spasticity spectrum, with just under 20% showing a prevalently pure spastic phenotype and just over 20% presenting congenital ataxias.

Abstract

Background: Monoallelic variants in the KIF1A gene are associated with a large set of clinical phenotypes including neurodevelopmental and neurodegenerative disorders, underpinned by a broad spectrum of central and peripheral nervous system involvement.

Methods: In a multicenter study conducted in patients presenting spastic gait or complex neurodevelopmental disorders, we analyzed the clinical, genetic and neuroradiological features of 28 index cases harboring heterozygous variants in KIF1A. We conducted a literature systematic review with the aim to comparing our findings with previously reported KIF1A-related phenotypes.

Results: Among 28 patients, we identified nine novel monoallelic variants, and one a copy number variation encompassing KIF1A. Mutations arose de novo in most patients and were prevalently located in the motor domain. Most patients presented features of a continuum ataxia-spasticity spectrum with only five cases showing a prevalently pure spastic phenotype and six presenting congenital ataxias. Seventeen mutations occurred in the motor domain of the Kinesin-1A protein, but location of mutation did not correlate with neurological and imaging presentations. When tested in 15 patients, muscle biopsy showed oxidative metabolism alterations (6 cases), impaired respiratory chain complexes II + III activity (3/6) and low CoQ10 levels (6/9). Ubiquinol supplementation (1gr/die) was used in 6 patients with subjective benefit.

Conclusions: This study broadened our clinical, genetic, and neuroimaging knowledge of KIF1A-related disorders. Although highly heterogeneous, it seems that manifestations of ataxia-spasticity spectrum disorders seem to occur in most patients. Some patients also present secondary impairment of oxidative metabolism; in this subset, ubiquinol supplementation therapy might be appropriate.

Monoallelic KIF1A-related disorders: a multicenter cross sectional study and systematic literature review

Stefania Della Vecchia 1 , Alessandra Tessa 2 , Claudia Dosi 3 , Jacopo Baldacci 4 , Rosa Pasquariello 1 , Antonella Antenora 5 , Guja Astrea 1 , Maria Teresa Bassi 6 , Roberta Battini 1 7 , Carlo Casali 8 , Ettore Cioffi 8 , Greta Conti 9 , Giovanna De Michele 5 , Anna Rita Ferrari 1 , Alessandro Filla 5 , Chiara Fiorillo 10 , Carlo Fusco 11 , Salvatore Gallone 12 , Chiara Germiniasi 13 , Renzo Guerrini 9 , Shalom Haggiag 14 , Diego Lopergolo 1 15 , Andrea Martinuzzi 16 , Federico Melani 9 , Andrea Mignarri 15 , Elena Panzeri 6 , Antonella Pini 17 , Anna Maria Pinto 18 , Francesca Pochiero 19 , Guido Primiano 20 , Elena Procopio 19 , Alessandra Renieri 18 , Romina Romaniello 21 , Cristina Sancricca 20 , Serenella Servidei 20 22 , Carlotta Spagnoli 11 , Chiara Ticci 1 19 , Anna Rubegni 1 , Filippo Maria Santorelli 23

1. IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.

2. IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy. [email protected].

3. Child Neurology, Fondazione IRCCS Istituto Neurologico Carlo Besta, 20133, Milan, Italy.

4. Kode Solutions, Lungarno Galileo Galilei 1, 56125, Pisa, Italy.

5. Department of Neurosciences, Reproductive and Odontostomatological Sciences, Federico II University, 80131, Naples, Italy.

6. Laboratory of Molecular Biology, Scientific Institute IRCCS Eugenio Medea, Bosisio Parini, 23842, Lecco, Italy.

7. Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, 56125, Pisa, Italy.

8. Department of Medical and Surgical Sciences and Biotechnologies, Sapienza University of Rome, 40100, Latina, Italy.

9. Neurology Unit and Neurogenetics Laboratories, Meyer Children University Hospital, University of Florence, 50139, Florence, Italy.

10. Neuromuscular Disorders Unit, IRCCS Istituto Giannina Gaslini, DINOGMI, University of Genoa, Genoa, Italy.

11. Child Neurology Unit, Pediatric Neurophysiology Laboratory, Department of Pediatrics, Azienda USL-IRCCS Di Reggio Emilia, 42122, Reggio Emilia, Italy.

12. Clinical Neurogenetics, Department Neurosciences, Az. Osp. Città della Salute e della Scienza di Torino, 1026, Torino, Italy.

13. Neuromuscular Unit, Scientific Institute IRCCS E. Medea, Bosisio Parini, 23842, Lecco, Italy.

14. Department of Neurology, Azienda Ospedaliera San Camillo Forlanini, 00152, Rome, Italy.

15. Unit of Neurology and Neurometabolic Disorders, Department of Medicine, Surgery and Neurosciences, University of Siena, 53100, Siena, Italy.

16. Scientific Institute IRCCS E. Medea, Unità Operativa Conegliano, 31015, Treviso, Italy.

17. Neuromuscular Pediatric Unit, IRRCS Istituto delle Scienze Neurologiche di Bologna, 40139, Bologna, Italy.

18. Medical Genetics Unit, University of Siena, Azienda Ospedaliera Universitaria Senese, 53100, Siena, Italy.

19. Department of Metabolic and Muscular, Meyer Children’s University Hospital, 50139, Florence, Italy.

20. Neurofisiopathology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168, Rome, Italy.

21. Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, 23842, Lecco, Italy.

22. Dipartimento Universitario di Neuroscienze, Università Cattolica del Sacro Cuore, 00168, Rome, Italy.

23. IRCCS Stella Maris Foundation, Calambrone, via dei Giacinti 2, 56128, Pisa, Italy.

Five cases of very rare SPG21 HSP studied

Originally described in the Amish community, cases of this complicated form of HSP have now been reported in Japanese, Italian, and from this study, German and Austrian families.

Background: Mast syndrome is a rare disorder belonging to the group of hereditary spastic paraplegias (HSPs). It is caused by bi-allelic mutations in the ACP33 gene, and is originally described in Old Order Amish. Outside this population, only one Japanese and one Italian family have been reported. Herein, we describe five subjects from the first three SPG21 families of German and Austrian descent.

Methods: Five subjects with complicated HSP were referred to our centers. The workup consisted of neurological examination, neurophysiological and neuropsychological assessments, MRI, and genetic testing.

Results: Onset varied from child- to adulthood. All patients exhibited predominant spastic para- or tetraparesis with positive pyramidal signs, pronounced cognitive impairment, ataxia, and extrapyramidal signs. Neurophysiological workup showed abnormal motor and sensory evoked potentials in all the patients. Sensorimotor axonal neuropathy was present in one patient. Imaging exhibited thin corpus callosum and global brain atrophy. Genetic testing revealed one heterozygous compound and two homozygous mutations in the ACP33 gene.

Conclusion: Herein, we report the first three Austrian and two German patients with SPG21, presenting a detailed description of their clinical phenotype and disease course. Our report adds to the knowledge of this extremely rare disorder, and highlights that SPG21 must also be considered in the differential diagnosis of complicated HSP outside the Amish community.

SOURCE: Front Neurol. 2022 Jan 17;12:799953. doi: 10.3389/fneur.2021.799953. eCollection 2021. PMID: 35111129 Copyright © 2022 Amprosi, Indelicato, Nachbauer, Hussl, Stendel, Eigentler, Gallenmüller, Boesch and Klopstock.

Mast Syndrome Outside the Amish Community: SPG21 in Europe

Matthias Amprosi 1 , Elisabetta Indelicato 1 , Wolfgang Nachbauer 1 , Anna Hussl 1 , Claudia Stendel 2 3 , Andreas Eigentler 1 , Constanze Gallenmüller 2 , Sylvia Boesch 1 , Thomas Klopstock 2 3 4

1. Department of Neurology, Center for Rare Neurological Movement Disorders, Medical University Innsbruck, Innsbruck, Austria.

2. Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-University Munich, Munich, Germany.

3. German Center for Neurodegenerative Diseases (DZNE), Munich, Germany.

4. Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.

SYNRG a new candidate gene for HSP

A variant detected in the SYNRG gene, in interaction with AP-1 in the AP complex family, may cause the complex HSP phenotype found in three people with this variant.

Background: Today, it is known that about 80 genes are involved in the aetiology of hereditary spastic paraplegia. However, there are many cases whose etiology could not be determined by extensive genetic tests such as whole-exome sequencing, clinical exome.

Methods: Candidate genes were determined, since no clinically illuminating variant was detected in the whole-exome sequencing analysis of three patients, two of whom were siblings, with a complex hereditary spastic paraplegia phenotype.

Results: The p.Leu1202Pro variant in the SYNRG gene in the 1st and 2nd cases, and the p.Gly533* variant in the 3rd case were homozygous.

Discussion: We suggest that the SYNRG gene interacting with AP-1 (adaptor-related protein) from the AP complex family may cause the complex hereditary spastic paraplegia phenotype with extensive clinical spectrum. It may be important to evaluate SYNRG gene variants in patients with hereditary spastic paraplegia whose aetiology has not been clarified.

SOURCE: Brain Dev. 2022 Jan 25;S0387-7604(22)00004-3. doi: 10.1016/j.braindev.2022.01.002. Online ahead of print. PMID: 35090779 Copyright © 2022 The Japanese Society of Child Neurology. Published by Elsevier B.V. All rights reserved.

Interacting with AP1 complex mutated synergin gamma (SYNRG) reveals a novel coatopathy in the form of complicated hereditary spastic paraplegia

Akif Ayaz 1 , Tugce Aksu Uzunhan 2 , Kursad Aydin 3

1. Department of Medical Genetics, Istanbul Medipol University, Faculty of Medicine, Istanbul, Turkey.

2. Department of Pediatric Neurology, Prof Dr. Cemil Taşcıoğlu City Hospital, University of Health Sciences, Istanbul, Turkey.

3. Department of Pediatric Neurology, Istanbul Medipol University, Faculty of Medicine, Istanbul, Turkey.

New variant discovered in RNF170 gene

Causing recessive SPG85 in a 7-year-old girl

Abstract

Hereditary spastic paraplegia (HSP) refers to a group of genetic disorders characterized by progressive weakness and stiffness in the muscles of the legs. To date, more than 83 types of HSP exist, differing in their etiology, their degree of severity, and the nature of symptoms associated with each of these conditions. Owing to their genetic and clinical heterogeneity, the establishment of an accurate diagnosis can be very challenging, especially with the clinical overlap observed between those conditions and other neurogenetic diseases.

A 7-year-old girl, born to a consanguineous Iraqi family, was referred to us for clinical and genetic evaluation. The patient presents with progressive difficulty in walking that started when she was 3 years old, lower limb predominant spastic paraparesis, and mild upper limbs involvement with slight tremor in the hands, all occurring in the absence of neurodevelopmental or growth delays.

Whole exome sequencing revealed a novel homozygous missense variation in the RNF170 gene (NM_030954.3; p.Cys107Trp), thus establishing the diagnosis of HSP. Here, we report the second missense biallelic variation in RNF170 and we discuss thoroughly all previously reported cases with RNF170-linked HSP.

SOURCE: Neurogenetics. 2022 Jan 18. doi: 10.1007/s10048-022-00685-6. Online ahead of print. PMID: 35041108 © 2022. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.

A novel homozygous variant in RNF170 causes hereditary spastic paraplegia: a case report and review of the literature

Eliane Chouery 1 , Cybel Mehawej 1 , Andre Megarbane 2 3

1. Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.

2. Department of Human Genetics, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.

3. Institut Jérôme Lejeune, Paris, France.

Two variants in the AP4B1 gene discovered

One confirmed as pathogenic causing SPG47

Abstract

Pathogenic variants in the AP4B1 gene lead to a rare form of hereditary spastic paraplegia (HSP) known as SPG47. We report on a patient with a clinical suspicion of complicated HSP of the lower limbs with intellectual disability, as well as a novel homozygous noncanonical splice site variant in the AP4B1 gene, in which the effect on splicing was validated by RNA analysis.

We sequenced 152 genes associated with HSP using Next-Generation Sequencing (NGS). We isolated total RNA from peripheral blood and generated cDNA using reverse transcription-polymerase chain reaction (RT-PCR). A region of AP4B1 mRNA was amplified by PCR and the fragments obtained were purified from the agarose gel and sequenced. We found a homozygous variant of uncertain significance in the AP4B1 gene NM_006594.4: c.1511-6C>G in the proband. Two different AP4B1 mRNA fragments were obtained in the patient and his carrier parents. The shorter fragment was the predominant fragment in the patient and revealed a deletion with skipping of the AP4B1 exon 10. The patient’s longer fragment corresponded to an insertion of the last five nucleotides of AP4B1 intron 9. We confirmed that this variant affects the normal splicing of RNA, sustaining the molecular diagnosis of SPG47 in the patient.