De Novo Mutations in Moderate or Severe Intellectual Disability

PLoS Genetics

Volumn 10, Issue 10, 2014, Pages

  Hamdan, Fadi F ^a   Srour, Myriam ^a,b   Capo Chichi, Jose Mario ^a   Daoud, Hussein ^c   Nassif, Christina ^a   Patry, Lysanne ^a   Massicotte, Christine ^a   Ambalavanan, Amirthagowri ^c   Spiegelman, Dan ^c   Diallo, Ousmane ^c   Henrion, Edouard ^c   Dionne Laporte, Alexandre ^c   Fougerat, Anne ^a   Pshezhetsky, Alexey V ^a   Venkateswaran, Sunita ^d   Rouleau, Guy A ^c   Michaud, Jacques L ^a,e  

^a UNIVERSITY OF MONTREAL   (Canada)

^b MONTREAL CHILDREN S HOSPITAL   (Canada)

^c MCGILL UNIVERSITY   (Canada)

^d CHILDREN S HOSPITAL OF EASTERN ONTARIO   (Canada)

^e UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR BETA3; ARGONAUTE 1 PROTEIN; EARLY GROWTH RESPONSE FACTOR 1; GENOMIC DNA; N METHYL DEXTRO ASPARTIC ACID RECEPTOR 2B; RYANODINE RECEPTOR 2; STOP CODON;

ARID1B GENE; ARTICLE; CHD2 GENE; CHMP2A GENE; CLINICAL ARTICLE; COL4A3BP GENE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DE NOVO MUTATION; DIAGNOSTIC VALUE; DISEASE SEVERITY; EGR1 GENE; EIF2C1 GENE; EXOME; FEMALE; FOXG1 GENE; FRAMESHIFT MUTATION; GABRB3 GENE; GATAD2B GENE; GENE; GENE DELETION; GENE IDENTIFICATION; GENE INSERTION; GENE INTERACTION; GENE MUTATION; GENETIC ASSOCIATION; GENETIC VARIABILITY; GRIN2B GENE; HNRNPU GENE; HUMAN; INTELLECTUAL IMPAIRMENT; LOSS OF FUNCTION MUTATION; MALE; MBD5 GENE; MED13L GENE; MISSENSE MUTATION; MOLECULAR PATHOLOGY; MYH10 GENE; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PARENT; PPP1CB GENE; PPP2R2B GENE; PROTEIN ANALYSIS; PROTEIN PROTEIN INTERACTION; RNA SPLICING; RYR2 GENE; SEQUENCE ANALYSIS; SET GENE; SETBP1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; TBR1 GENE; TCF4 GENE; VPS4A GENE; WAC GENE; WDR45 GENE; EPILEPSY; GENETICS; PATHOLOGY; POINT MUTATION; STOP CODON;

CODON, NONSENSE; EPILEPSY; EXOME; FRAMESHIFT MUTATION; HUMANS; INTELLECTUAL DISABILITY; MUTATION, MISSENSE; POINT MUTATION; RNA SPLICING; SEQUENCE DELETION;

EID: 84908314239     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004772     Document Type: Article

References (62)

1. Ropers HH, (2010) Genetics of early onset cognitive impairment. Annu Rev Genomics Hum Genet 11: 161–187.
2. de Ligt J, Willemsen MH, van Bon BW, Kleefstra T, Yntema HG, et al. (2012) Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med 367: 1921–1929.
3. Hamdan FF, Gauthier J, Araki Y, Lin DT, Yoshizawa Y, et al. (2011) Excess of de novo deleterious mutations in genes associated with glutamatergic systems in nonsyndromic intellectual disability. Am J Hum Genet 88: 306–316.
4. Rauch A, Wieczorek D, Graf E, Wieland T, Endele S, et al. (2012) Range of genetic mutations associated with severe non-syndromic sporadic intellectual disability: an exome sequencing study. Lancet 380: 1674–1682.
5. Vissers LE, de Ligt J, Gilissen C, Janssen I, Steehouwer M, et al. (2010) A de novo paradigm for mental retardation. Nat Genet 42: 1109–1112.
6. Epilepsy Phenome/Genome P, Allen AS, Berkovic SF, Cossette P, Epi4K Consortium (2013) et al. (2013) De novo mutations in epileptic encephalopathies. Nature 501: 217–221.
7. Iossifov I, Ronemus M, Levy D, Wang Z, Hakker I, et al. (2012) De novo gene disruptions in children on the autistic spectrum. Neuron 74: 285–299.
8. Neale BM, Kou Y, Liu L, Ma'ayan A, Samocha KE, et al. (2012) Patterns and rates of exonic de novo mutations in autism spectrum disorders. Nature 485: 242–245.
9. O'Roak BJ, Vives L, Girirajan S, Karakoc E, Krumm N, et al. (2012) Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485: 246–250.
10. Sanders SJ, Murtha MT, Gupta AR, Murdoch JD, Raubeson MJ, et al. (2012) De novo mutations revealed by whole-exome sequencing are strongly associated with autism. Nature 485: 237–241.
11. Xu B, Ionita-Laza I, Roos JL, Boone B, Woodrick S, et al. (2012) De novo gene mutations highlight patterns of genetic and neural complexity in schizophrenia. Nat Genet 44: 1365–1369.
12. Hoyer J, Ekici AB, Endele S, Popp B, Zweier C, et al. (2012) Haploinsufficiency of ARID1B, a member of the SWI/SNF-a chromatin-remodeling complex, is a frequent cause of intellectual disability. Am J Hum Genet 90: 565–572.
13. Carvill GL, Heavin SB, Yendle SC, McMahon JM, O'Roak BJ, et al. (2013) Targeted resequencing in epileptic encephalopathies identifies de novo mutations in CHD2 and SYNGAP1. Nat Genet 45: 825–830.
14. Kortum F, Das S, Flindt M, Morris-Rosendahl DJ, Stefanova I, et al. (2011) The core FOXG1 syndrome phenotype consists of postnatal microcephaly, severe mental retardation, absent language, dyskinesia, and corpus callosum hypogenesis. J Med Genet 48: 396–406.
15. Willemsen MH, Nijhof B, Fenckova M, Nillesen WM, Bongers EM, et al. (2013) GATAD2B loss-of-function mutations cause a recognisable syndrome with intellectual disability and are associated with learning deficits and synaptic undergrowth in Drosophila. J Med Genet 50: 507–514.
16. Bonnet C, Ali Khan A, Bresso E, Vigouroux C, Beri M, et al. (2013) Extended spectrum of MBD5 mutations in neurodevelopmental disorders. Eur J Hum Genet 21: 1457–1461.
17. Talkowski ME, Mullegama SV, Rosenfeld JA, van Bon BW, Shen Y, et al. (2011) Assessment of 2q23.1 microdeletion syndrome implicates MBD5 as a single causal locus of intellectual disability, epilepsy, and autism spectrum disorder. Am J Hum Genet 89: 551–563.
18. Kleefstra T, Kramer JM, Neveling K, Willemsen MH, Koemans TS, et al. (2012) Disruption of an EHMT1-associated chromatin-modification module causes intellectual disability. Am J Hum Genet 91: 73–82.
19. Asadollahi R, Oneda B, Sheth F, Azzarello-Burri S, Baldinger R, et al. (2013) Dosage changes of MED13L further delineate its role in congenital heart defects and intellectual disability. Eur J Hum Genet 21: 1100–1104.
20. van Haelst MM, Monroe GR, Duran K, van Binsbergen E, Breur JM, et al. (2014) Further confirmation of the MED13L haploinsufficiency syndrome. Eur J Hum Genet
21. Gilissen C, Hehir-Kwa JY, Thung DT, van de Vorst M, van Bon BW, et al. (2014) Genome sequencing identifies major causes of severe intellectual disability. Nature 511: 344–347.
22. Hoischen A, van Bon BW, Gilissen C, Arts P, van Lier B, et al. (2010) De novo mutations of SETBP1 cause Schinzel-Giedion syndrome. Nat Genet 42: 483–485.
23. Hamdan FF, Daoud H, Patry L, Dionne-Laporte A, Spiegelman D, et al. (2013) Parent-child exome sequencing identifies a de novo truncating mutation in TCF4 in non-syndromic intellectual disability. Clin Genet 83: 198–200.
24. Need AC, Shashi V, Hitomi Y, Schoch K, Shianna KV, et al. (2012) Clinical application of exome sequencing in undiagnosed genetic conditions. J Med Genet 49: 353–361.
25. Zweier C, Peippo MM, Hoyer J, Sousa S, Bottani A, et al. (2007) Haploinsufficiency of TCF4 causes syndromal mental retardation with intermittent hyperventilation (Pitt-Hopkins syndrome). Am J Hum Genet 80: 994–1001.
26. Haack TB, Hogarth P, Kruer MC, Gregory A, Wieland T, et al. (2012) Exome sequencing reveals de novo WDR45 mutations causing a phenotypically distinct, X-linked dominant form of NBIA. Am J Hum Genet 91: 1144–1149.
27. Saitsu H, Nishimura T, Muramatsu K, Kodera H, Kumada S, et al. (2013) De novo mutations in the autophagy gene WDR45 cause static encephalopathy of childhood with neurodegeneration in adulthood. Nat Genet 45: 445–449, 449e441.
28. Filges I, Shimojima K, Okamoto N, Rothlisberger B, Weber P, et al. (2011) Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel-Giedion syndrome. J Med Genet 48: 117–122.
29. O'Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, et al. (2012) Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 338: 1619–1622.
30. Palumbo O, Fichera M, Palumbo P, Rizzo R, Mazzolla E, et al. (2014) TBR1 is the candidate gene for intellectual disability in patients with a 2q24.2 interstitial deletion. Am J Med Genet A 164(A): 828–833.
31. Endele S, Rosenberger G, Geider K, Popp B, Tamer C, et al. (2010) Mutations in GRIN2A and GRIN2B encoding regulatory subunits of NMDA receptors cause variable neurodevelopmental phenotypes. Nat Genet 42: 1021–1026.
32. Lemke JR, Hendrickx R, Geider K, Laube B, Schwake M, et al. (2014) GRIN2B mutations in West syndrome and intellectual disability with focal epilepsy. Ann Neurol 75: 147–154.
33. Ballif BC, Rosenfeld JA, Traylor R, Theisen A, Bader PI, et al. (2012) High-resolution array CGH defines critical regions and candidate genes for microcephaly, abnormalities of the corpus callosum, and seizure phenotypes in patients with microdeletions of 1q43q44. Hum Genet 131: 145–156.
34. Thierry G, Beneteau C, Pichon O, Flori E, Isidor B, et al. (2012) Molecular characterization of 1q44 microdeletion in 11 patients reveals three candidate genes for intellectual disability and seizures. Am J Med Genet A 158A: 1633–1640.
35. Isken O, Maquat LE, (2007) Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function. Genes Dev 21: 1833–1856.
36. Zhang F, Yu X, (2011) WAC, a functional partner of RNF20/40, regulates histone H2B ubiquitination and gene transcription. Mol Cell 41: 384–397.
37. Wentzel C, Rajcan-Separovic E, Ruivenkamp CA, Chantot-Bastaraud S, Metay C, et al. (2011) Genomic and clinical characteristics of six patients with partially overlapping interstitial deletions at 10p12p11. Eur J Hum Genet 19: 959–964.
38. Venetucci L, Denegri M, Napolitano C, Priori SG, (2012) Inherited calcium channelopathies in the pathophysiology of arrhythmias. Nat Rev Cardiol 9: 561–575.
39. Van Petegem F, (2012) Ryanodine receptors: structure and function. J Biol Chem 287: 31624–31632.
40. LaPage MJ, Russell MW, Bradley DJ, Dick M, 2nd (2012) Novel ryanodine receptor 2 mutation associated with a severe phenotype of catecholaminergic polymorphic ventricular tachycardia. J Pediatr 161: 362–364.
41. Johnson JN, Tester DJ, Bass NE, Ackerman MJ, (2010) Cardiac channel molecular autopsy for sudden unexpected death in epilepsy. J Child Neurol 25: 916–921.
42. Lehnart SE, Mongillo M, Bellinger A, Lindegger N, Chen BX, et al. (2008) Leaky Ca2+ release channel/ryanodine receptor 2 causes seizures and sudden cardiac death in mice. J Clin Invest 118: 2230–2245.
43. Takano K, Liu D, Tarpey P, Gallant E, Lam A, et al. (2012) An X-linked channelopathy with cardiomegaly due to a CLIC2 mutation enhancing ryanodine receptor channel activity. Hum Mol Genet 21: 4497–4507.
44. Ma X, Bao J, Adelstein RS, (2007) Loss of cell adhesion causes hydrocephalus in nonmuscle myosin II-B-ablated and mutated mice. Mol Biol Cell 18: 2305–2312.
45. Ma X, Kawamoto S, Hara Y, Adelstein RS, (2004) A point mutation in the motor domain of nonmuscle myosin II-B impairs migration of distinct groups of neurons. Mol Biol Cell 15: 2568–2579.
46. Tuzovic L, Yu L, Zeng W, Li X, Lu H, et al. (2013) A human de novo mutation in MYH10 phenocopies the loss of function mutation in mice. Rare Dis 1: e26144.
47. Muto S, Senda M, Akai Y, Sato L, Suzuki T, et al. (2007) Relationship between the structure of SET/TAF-Ibeta/INHAT and its histone chaperone activity. Proc Natl Acad Sci U S A 104: 4285–4290.
48. Minakuchi M, Kakazu N, Gorrin-Rivas MJ, Abe T, Copeland TD, et al. (2001) Identification and characterization of SEB, a novel protein that binds to the acute undifferentiated leukemia-associated protein SET. Eur J Biochem 268: 1340–1351.
49. Leung JW, Leitch A, Wood JL, Shaw-Smith C, Metcalfe K, et al. (2011) SET nuclear oncogene associates with microcephalin/MCPH1 and regulates chromosome condensation. J Biol Chem 286: 21393–21400.
50. Jackson AP, Eastwood H, Bell SM, Adu J, Toomes C, et al. (2002) Identification of microcephalin, a protein implicated in determining the size of the human brain. Am J Hum Genet 71: 136–142.
51. Poirier R, Cheval H, Mailhes C, Garel S, Charnay P, et al. (2008) Distinct functions of egr gene family members in cognitive processes. Front Neurosci 2: 47–55.
52. Bozon B, Davis S, Laroche S, (2002) Regulated transcription of the immediate-early gene Zif268: mechanisms and gene dosage-dependent function in synaptic plasticity and memory formation. Hippocampus 12: 570–577.
53. Jones MW, Errington ML, French PJ, Fine A, Bliss TV, et al. (2001) A requirement for the immediate early gene Zif268 in the expression of late LTP and long-term memories. Nat Neurosci 4: 289–296.
54. Dickey AS, Strack S, (2011) PKA/AKAP1 and PP2A/Bbeta2 regulate neuronal morphogenesis via Drp1 phosphorylation and mitochondrial bioenergetics. J Neurosci 31: 15716–15726.
55. Munton RP, Vizi S, Mansuy IM, (2004) The role of protein phosphatase-1 in the modulation of synaptic and structural plasticity. FEBS Lett 567: 121–128.
56. Stuchell-Brereton MD, Skalicky JJ, Kieffer C, Karren MA, Ghaffarian S, et al. (2007) ESCRT-III recognition by VPS4 ATPases. Nature 449: 740–744.
57. McCullough J, Colf LA, Sundquist WI, (2013) Membrane fission reactions of the mammalian ESCRT pathway. Annu Rev Biochem 82: 663–692.
58. Morita E, Colf LA, Karren MA, Sandrin V, Rodesch CK, et al. (2010) Human ESCRT-III and VPS4 proteins are required for centrosome and spindle maintenance. Proc Natl Acad Sci U S A 107: 12889–12894.
59. Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, et al. (2013) GeneMANIA prediction server 2013 update. Nucleic Acids Res 41: W115–122.
60. Froyen G, Corbett M, Vandewalle J, Jarvela I, Lawrence O, et al. (2008) Submicroscopic duplications of the hydroxysteroid dehydrogenase HSD17B10 and the E3 ubiquitin ligase HUWE1 are associated with mental retardation. Am J Hum Genet 82: 432–443.
61. Wang K, Li M, Hakonarson H, (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38: e164.
62. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nat Biotechnol 29: 24–26.