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A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome

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Abstract

Cohen syndrome is caused by homozygous mutation in the vacuolar protein sorting 13 homolog B (VPS13B, also referred to as COH1) gene on chromosome 8q22.2. The VPS13B protein is involved in transmembrane transport, Golgi integrity, and neuritogenesis. Clinical manifestations of Cohen syndrome are mainly intellectual disability, developmental delay, facial abnormalities, and eye disorders. This study aimed to identify the causative variant in two unrelated families with Cohen syndrome. To this end, whole-exome sequencing (WES) was performed to identify the pathogenic variants. A homozygous nonsense variant (NM_017890:c.10369C > T; NP_060360.3: p.Q3457X) in the VPS13B gene was identified and co-segregated with all affected individuals in both families. In silico analysis highly suggested this variant as damaging for protein function. The present study increases the mutation spectrum of the VPS13B gene and could be useful in genetic diagnosis and genetic counseling in Cohen syndrome patients.

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References

  • Alipour N, Salehpour S, Tonekaboni SH, Rostami M, Bahari S, Yassaee V et al (2020) Mutations in the VPS13B Gene in Iranian Patients with Different Phenotypes of Cohen Syndrome. J Mol Neurosci [Internet] 70(1):21–5. Available from: http://link.springer.com/10.1007/s12031-019-01394-w

  • Amendola LM, Jarvik GP, Leo MC, McLaughlin HM, Akkari Y, Amaral MD et al (2016) Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium. Am J Hum Genet [Internet] 98(6):1067–76. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0002929716300593

  • Bugiani M, Gyftodimou Y, Tsimpouka P, Lamantea E, Katzaki E, D’Adamo P et al (2008) Cohen syndrome resulting from a novel large intragenic COH1 deletion segregating in an isolated Greek island population. Am J Med Genet Part A 146(17):2221–2226

    Article  Google Scholar 

  • Carey JC, Hall BD (1978) Confirmation of the Cohen syndrome. J Pediatr [Internet] 93(2):239–44. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0022347678805046

  • Chandler KE (2003) Diagnostic criteria, clinical characteristics, and natural history of Cohen syndrome. J Med Genet [Internet] 40(4):233–41. Available from: https://jmg.bmj.com/lookup/doi/10.1136/jmg.40.4.233

  • Darvish H, Bravo P, Tafakhori A, Azcona LJ, Ranji-Burachaloo S, Johari AH et al  (2018) Identification of a large homozygous VPS13C deletion in a patient with early-onset Parkinsonism. Mov Disord [Internet] 33(12):1968–70. Available from: http://www.ncbi.nlm.nih.gov/pubmed/30452786

  • Dastan J, Chijiwa C, Tang F, Martell S, Qiao Y, Rajcan-Separovic E et al (2016) Exome sequencing identifies pathogenic variants of VPS13B in a patient with familial 16p11.2 duplication. BMC Med Genet [Internet] 17(1):1–6. Available from: http://dx.doi.org/10.1186/s12881-016-0340

  • Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S (2010) Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++. Wasserman WW, editor. PLoS Comput Biol [Internet] 6(12):e1001025. Available from: https://dx.plos.org/10.1371/journal.pcbi.1001025

  • Douzgou S, Petersen M (2011) Clinical variability of genetic isolates of Cohen syndrome. Clin Genet [Internet] 79(6):501–6. Available from: http://doi.wiley.com/10.1111/j.1399-0004.2011.01669.x

  • Duplomb L, Duvet S, Picot D, Jego G, El Chehadeh-Djebbar S, Marle N et al (2014) Cohen syndrome is associated with major glycosylation defects. Hum Mol Genet [Internet] 23(9):2391–9. Available from: http://www.ncbi.nlm.nih.gov/pubmed/24334764

  • Falk MJ, Feiler HS, Neilson DE, Maxwell K, Lee JV, Segall SK et al  (2004) Cohen syndrome in the Ohio Amish. Am J Med Genet Part A [Internet] 128A(1):23–8. Available from: http://doi.wiley.com/10.1002/ajmg.a.30033

  • Gauthier J, Meijer IA, Lessel D, Mencacci NE, Krainc D, Hempel M et al (2018) Recessive mutations in VPS13D cause childhood onset movement disorders. Ann Neurol [Internet] 83(6):1089–95. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/ana.25204

  • Horn D, Krebsov A, Kunze J, Reis A (2000) Homozygosity mapping in a family with microcephaly, mental retardation, and short stature to a Cohen syndrome region on 8q21.3 - 8q22.1: Redefining a clinical entity. Am J Med Genet [Internet] 92(4):285–92. Available from:  https://onlinelibrary.wiley.com/10.1002/(SICI)1096-8628(20000605)92:4%3C285::AID-AJMG13%3E3.0.CO;2-D

  • Kaushik P, Mahajan N, Girimaji SC, Kumar A (2020) Whole exome sequencing identifies a novel homozygous duplication mutation in the VPS13B gene in an Indian family with cohen syndrome. J Mol Neurosci [Internet] 70(8):1225–8. Available from: http://link.springer.com/10.1007/s12031-020-01530-x

  • Kivitie-Kallio S, Summanen P, Raitta C, Norio R (2000) Ophthalmologic findings in Cohen syndrome. Ophthalmology [Internet] 107(9):1737–45. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0161642000002797

  • Kivitie-Kallio S, Norio R (2001) Cohen syndrome: essential features, natural history, and heterogeneity. Am J Med Genet [Internet] 102(2):125–35. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11477603

  • Koehler K, Schuelke M, Hell AK, Schittkowski M, Huebner A, Brockmann K (2020) A novel homozygous nonsense mutation of VPS13B associated with previously unreported features of Cohen syndrome. Am J Med Genet Part A [Internet] 182(3):570–5. Available from: https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.61435

  • Kolehmainen J, Black GCM, Saarinen A, Chandler K, Clayton-smith J, Tra A et al (2003) Cohen syndrome is caused by mutations in a novel gene COH1 encoding a transmembrane protein with a presumed role in vesicle-mediated sorting and intracellular protein transport 1359–69

  • Lesage S, Drouet V, Majounie E, Deramecourt V, Jacoupy M, Nicolas A et al (2016) Loss of VPS13C function in autosomal-recessive parkinsonism causes mitochondrial dysfunction and increases PINK1/parkin-dependent mitophagy. Am J Hum Genet [Internet] 98(3):500–13. Available from: http://www.ncbi.nlm.nih.gov/pubmed/26942284

  • Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics [Internet] 25(14):1754–60. Available from: https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btp324

  • Lupo F, Tibaldi E, Matte A, Sharma AK, Brunati AM, Alper SL et al (2016) A new molecular link between defective autophagy and erythroid abnormalities in chorea-acanthocytosis. Blood [Internet] 128(25):2976–87. Available from: https://ashpublications.org/blood/article/128/25/2976/35676/A-new-molecular-link-between-defective-autophagy

  • Michael Cohen M, Hall BD, Smith DW, Benjamin Graham C, Lampert KJ (1973) A new syndrome with hypotonia, obesity, mental deficiency, and facial, oral, ocular, and limb anomalies. J Pediatr [Internet] 83(2):280–4. Available from: https://linkinghub.elsevier.com/retrieve/pii/S0022347673804937

  • Momtazmanesh S, Rayzan E, Shahkarami S, Rohlfs M, Klein C, Rezaei N (2020) A novel VPS13B mutation in Cohen syndrome: a case report and review of literature. BMC Med Genet [Internet] 21(1):140. Available from: https://bmcmedgenet.biomedcentral.com/articles/10.1186/s12881-020-01075-1

  • Pelzl L, Elsir B, Sahu I, Bissinger R, Singh Y, Sukkar B et al (2017) Lithium Sensitivity of Store Operated Ca2+ Entry and Survival of Fibroblasts Isolated from Chorea-Acanthocytosis Patients. Cell Physiol Biochem [Internet] 42(5):2066–77. Available from: https://www.karger.com/Article/FullText/479901

  • Quang D, Chen Y, Xie X (2015) DANN: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics [Internet] 31(5):761–3. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25338716

  • Rafiq MA, Leblond CS, Saqib MAN, Vincent AK, Ambalavanan A, Khan FS et al (2015) Novel VPS13B mutations in three large pakistani cohen syndrome families suggests a baloch variant with autistic-like features. BMC Med Genet [Internet] 16(1):41. Available from: http://bmcmedgenet.biomedcentral.com/articles/10.1186/s12881-015-0183-0

  • Rampoldi L, Dobson-Stone C, Rubio JP, Danek A, Chalmers RM, Wood NW et al (2001) A conserved sorting-associated protein is mutant in chorea-acanthocytosis. Nat Genet [Internet] 28(2):119–20. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11381253

  • Rejeb I, Jilani H, Elaribi Y, Hizem S, Hila L, Zillahrdt JL et al (2017) First case report of Cohen syndrome in the Tunisian population caused by VPS13B mutations. BMC Med Genet [Internet] 18(1):134. Available from: https://bmcmedgenet.biomedcentral.com/articles/10.1186/s12881-017-0493-5

  • Rodrigues JM, Fernandes HD, Caruthers C, Braddock SR, Knutsen AP (2018) Cohen Syndrome: Review of the Literature. Cureus [Internet] Available from: https://www.cureus.com/articles/14437-cohen-syndrome-review-of-the-literature

  • Rogers MF, Shihab HA, Mort M, Cooper DN, Gaunt TR, Campbell C (2018) FATHMM-XF: accurate prediction of pathogenic point mutations via extended features. Hancock J, editor. Bioinformatics [Internet] 34(3):511–3. Available from: https://academic.oup.com/bioinformatics/article/34/3/511/4104409

  • Rzepnikowska W, Flis K, Muñoz-Braceras S, Menezes R, Escalante R, Zoladek T (2017) Yeast and other lower eukaryotic organisms for studies of Vps13 proteins in health and disease. Traffic [Internet] 18(11):711–9. Available from: http://doi.wiley.com/10.1111/tra.12523

  • Schormair B, Kemlink D, Mollenhauer B, Fiala O, Machetanz G, Roth J et al (2018) Diagnostic exome sequencing in early-onset Parkinson’s disease confirms VPS13C as a rare cause of autosomal-recessive Parkinson’s disease. Clin Genet [Internet] 93(3):603–12. Available from: http://www.ncbi.nlm.nih.gov/pubmed/28862745

  • de Summa S, Malerba G, Pinto R, Mori A, Mijatovic V, Tommasi S (2017) GATK hard filtering: tunable parameters to improve variant calling for next generation sequencing targeted gene panel data. BMC Bioinformatics [Internet] 18(S5):119. Available from: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1537-8

  • Seifert W, Holder-Espinasse M, Kühnisch J, Kahrizi K, Tzschach A, Garshasbi M et al (2009) Expanded mutational spectrum in Cohen syndrome, tissue expression, and transcript variants of COH1. Hum Mutat [Internet] 30(2):E404–20. Available from: http://doi.wiley.com/10.1002/humu.20886

  • Seifert W, Kühnisch J, Maritzen T, Horn D, Haucke V, Hennies HC (2011) Cohen syndrome-associated protein, COH1, is a novel, giant Golgi matrix protein required for Golgi integrity. J Biol Chem [Internet] 286(43):37665–75. Available from: http://www.ncbi.nlm.nih.gov/pubmed/21865173

  • Seifert W, Kühnisch J, Maritzen T, Lommatzsch S, Hennies HC, Bachmann S et al (2015) Cohen syndrome-associated protein COH1 physically and functionally interacts with the small GTPase RAB6 at the Golgi complex and directs neurite outgrowth. J Biol Chem [Internet] 290(6):3349–58. Available from: http://www.ncbi.nlm.nih.gov/pubmed/25492866

  • Seong E, Insolera R, Dulovic M, Kamsteeg E-J, Trinh J, Brüggemann N et al (2018) Mutations in VPS13D lead to a new recessive ataxia with spasticity and mitochondrial defects. Ann Neurol [Internet] 83(6):1075–88. Available from: http://www.ncbi.nlm.nih.gov/pubmed/29604224

  • Sim N, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC (2012) SIFT web server : predicting effects of amino acid substitutions on proteins 40:452–457

    Google Scholar 

  • Taban M, Memoracion-Peralta DSA, Wang H, Al-Gazali LI, Traboulsi EI (2007) Cohen syndrome: Report of nine cases and review of the literature, with emphasis on ophthalmic features. J Am Assoc Pediatr Ophthalmol Strabismus [Internet] 11(5):431–7. Available from: https://linkinghub.elsevier.com/retrieve/pii/S1091853107001474

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res [Internet] 22(22):4673–80. Available from: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/22.22.4673

  • Ueno S, Maruki Y, Nakamura M, Tomemori Y, Kamae K, Tanabe H et al (2001) The gene encoding a newly discovered protein, chorein, is mutated in chorea-acanthocytosis. Nat Genet [Internet] 28(2):121–2. Available from: http://www.ncbi.nlm.nih.gov/pubmed/11381254

  • Velayos-baeza A, Vettori A, Copley RR, Dobson-stone C (2004) Analysis of the human VPS13 gene family 84:536–49

  • Yang H, Wang K (2015) Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc [Internet] 10(10):1556–66. Available from: http://www.nature.com/articles/nprot.2015.105

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Correspondence to Kolsoum Saeidi.

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The research project under the title of “A novel VPS13B mutation identified by whole-exome sequencing in Iranian patients with Cohen syndrome” was given ethical approval by the Bam University of Medical Sciences, Bam, Iran (no. IR.MUBAM.REC.1399.010).

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Karimzadeh, M.R., Omidi, F., Sahebalzamani, A. et al. A Novel VPS13B Mutation Identified by Whole-Exome Sequencing in Iranian Patients with Cohen Syndrome. J Mol Neurosci 71, 2566–2574 (2021). https://doi.org/10.1007/s12031-021-01852-4

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