Variations analysis of NLGN3 and NLGN4X gene in Chinese autism patients


Autism is a neurodevelopmental disorder clinically characterized by impairment of social interaction, deficits in verbal communication, as well as stereotypic and repetitive behaviors. Several studies have implicated that abnormal synaptogenesis was involved in the incidence of autism. Neuroligins are postsynaptic cell adhesion molecules and interacted with neurexins to regulate the fine balance between excitation and inhibition of synapses. Recently, mutation analysis, cellular and mice models hinted neuroligin mutations probably affected synapse maturation and function. In this study, four missense variations [p.G426S (NLGN3), p.G84R (NLGN4X), p.Q162 K (NLGN4X) and p.A283T (NLGN4X)] in four different unrelated patients have been identified by PCR and direct sequencing. These four missense variations were absent in the 453 controls and have not been reported in 1000 Genomes Project. Bioinformatic analysis of the four missense variations revealed that p.G84R and p.A283T were “Probably Damaging”. The variations may cause abnormal synaptic homeostasis and therefore trigger the patients more predisposed to autism. By case–control analysis, we identified the common SNPs (rs3747333 and rs3747334) in the NLGN4X gene significantly associated with risk for autism [p = 5.09E-005; OR 4.685 (95 % CI 2.073–10.592)]. Our data provided a further evidence for the involvement of NLGN3 and NLGN4X gene in the pathogenesis of autism in Chinese population.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2


  1. 1.

    Lainhart JE, Ozonoff S, Coon H, Krasny L, Dinh E, Nice J, McMahon W (2002) Autism, regression, and the broader autism phenotype. Am J Med Genet 113:231–237

    Article  PubMed  Google Scholar 

  2. 2.

    Keller F, Persico AM (2003) The neurobiological context of autism. Mol Neurobiol 28:1–22

    CAS  Article  PubMed  Google Scholar 

  3. 3.

    Volkmar FR, Pauls D (2003) Autism. Lancet 362:1133–1141

    Article  PubMed  Google Scholar 

  4. 4.

    Elsabbagh M, Divan G, Koh YJ, Kim YS, Kauchali S, Marcin C, Montiel-Nava C, Patel V, Paula CS, Wang C, Yasamy MT, Fombonne E (2012) Global prevalence of autism and other pervasive developmental disorders. Autism Res 5:160–179

    PubMed Central  Article  PubMed  Google Scholar 

  5. 5.

    Sutcliffe JS (2008) Genetics. Insights into the pathogenesis of autism. Science 321:208–209

    CAS  Article  PubMed  Google Scholar 

  6. 6.

    Bailey A, Le Couteur A, Gottesman I, Bolton P, Simonoff E, Yuzda E, Rutter M (1995) Autism as a strongly genetic disorder: evidence from a British twin study. Psychol Med 25:63–77

    CAS  Article  PubMed  Google Scholar 

  7. 7.

    Szatmari P, Jones MB, Zwaigenbaum L, MacLean JE (1998) Genetics of autism: overview and new directions. J Autism Dev Disord 28:351–368

    CAS  Article  PubMed  Google Scholar 

  8. 8.

    Rutter M (2000) Genetic studies of autism: from the 1970s into the millennium. J Abnorm Child Psychol 28:3–14

    CAS  Article  PubMed  Google Scholar 

  9. 9.

    Philippe A, Martinez M, Guilloud-Bataille M, Gillberg C, Rastam M, Sponheim E, Coleman M, Zappella M, Aschauer H, Van Maldergem L, Penet C, Feingold J, Brice A, Leboyer M (1999) Genome-wide scan for autism susceptibility genes. Paris Autism Research International Sibpair Study. Hum Mol Genet 8:805–812

    CAS  Article  PubMed  Google Scholar 

  10. 10.

    Jamain S, Quach H, Betancur C, Rastam M, Colineaux C, Gillberg IC, Soderstrom H, Giros B, Leboyer M, Gillberg C, Bourgeron T (2003) Mutations of the X-linked genes encoding neuroligins NLGN3 and NLGN4 are associated with autism. Nat Genet 34:27–29

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  11. 11.

    Laumonnier F, Bonnet-Brilhault F, Gomot M, Blanc R, David A, Moizard MP, Raynaud M, Ronce N, Lemonnier E, Calvas P, Laudier B, Chelly J, Fryns JP, Ropers HH, Hamel BC, Andres C, Barthelemy C, Moraine C, Briault S (2004) X-linked mental retardation and autism are associated with a mutation in the NLGN4 gene, a member of the neuroligin family. Am J Hum Genet 74:552–557

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  12. 12.

    Lawson-Yuen A, Saldivar JS, Sommer S, Picker J (2008) Familial deletion within NLGN4 associated with autism and Tourette syndrome. Eur J Hum Genet 16:614–618

    CAS  Article  PubMed  Google Scholar 

  13. 13.

    Thomas NS, Sharp AJ, Browne CE, Skuse D, Hardie C, Dennis NR (1999) Xp deletions associated with autism in three females. Hum Genet 104:43–48

    CAS  Article  PubMed  Google Scholar 

  14. 14.

    Ichtchenko K, Nguyen T, Sudhof TC (1996) Structures, alternative splicing, and neurexin binding of multiple neuroligins. J Biol Chem 271:2676–2682

    CAS  Article  PubMed  Google Scholar 

  15. 15.

    Levinson JN, El-Husseini A (2007) A crystal-clear interaction: relating neuroligin/neurexin complex structure to function at the synapse. Neuron 56:937–939

    CAS  Article  PubMed  Google Scholar 

  16. 16.

    Yan J, Feng J, Schroer R, Li W, Skinner C, Schwartz CE, Cook EH, Sommer SS Jr (2008) Analysis of the neuroligin 4Y gene in patients with autism. Psychiatr Genet 18:204–207

    Article  PubMed  Google Scholar 

  17. 17.

    Yan J, Oliveira G, Coutinho A, Yang C, Feng J, Katz C, Sram J, Bockholt A, Jones IR, Craddock N, Cook EH Jr, Vicente A, Sommer SS (2005) Analysis of the neuroligin 3 and 4 genes in autism and other neuropsychiatric patients. Mol Psychiatry 10:329–332

    CAS  Article  PubMed  Google Scholar 

  18. 18.

    Talebizadeh Z, Lam DY, Theodoro MF, Bittel DC, Lushington GH, Butler MG (2006) Novel splice isoforms for NLGN3 and NLGN4 with possible implications in autism. J Med Genet 43:e21

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  19. 19.

    Chih B, Afridi SK, Clark L, Scheiffele P (2004) Disorder-associated mutations lead to functional inactivation of neuroligins. Hum Mol Genet 13:1471–1477

    CAS  Article  PubMed  Google Scholar 

  20. 20.

    Daoud H, Bonnet-Brilhault F, Vedrine S, Demattei MV, Vourc’h P, Bayou N, Andres CR, Barthelemy C, Laumonnier F, Briault S (2009) Autism and nonsyndromic mental retardation associated with a de novo mutation in the NLGN4X gene promoter causing an increased expression level. Biol Psychiatry 66:906–910

    CAS  Article  PubMed  Google Scholar 

  21. 21.

    Zhang C, Milunsky JM, Newton S, Ko J, Zhao G, Maher TA, Tager-Flusberg H, Bolliger MF, Carter AS, Boucard AA, Powell CM, Sudhof TC (2009) A neuroligin-4 missense mutation associated with autism impairs neuroligin-4 folding and endoplasmic reticulum export. J Neurosci 29:10843–10854

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  22. 22.

    Ey E, Leblond CS, Bourgeron T (2011) Behavioral profiles of mouse models for autism spectrum disorders. Autism Res 4:5–16

    Article  PubMed  Google Scholar 

  23. 23.

    Liu Y, Hu Z, Xun G, Peng Y, Lu L, Xu X, Xiong Z, Xia L, Liu D, Li W, Zhao J, Xia K (2012) Mutation analysis of the NRXN1 gene in a Chinese autism cohort. J Psychiatr Res 46:630–634

    Article  PubMed  Google Scholar 

  24. 24.

    Li X, Hu Z, He Y, Xiong Z, Long Z, Peng Y, Bu F, Ling J, Xun G, Mo X, Pan Q, Zhao J, Xia K (2010) Association analysis of CNTNAP2 polymorphisms with autism in the Chinese Han population. Psychiatr Genet 20:113–117

    PubMed  Google Scholar 

  25. 25.

    Koehnke J, Jin X, Budreck EC, Posy S, Scheiffele P, Honig B, Shapiro L (2008) Crystal structure of the extracellular cholinesterase-like domain from neuroligin-2. Proc Natl Acad Sci USA 105:1873–1878

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  26. 26.

    Sudhof TC (2008) Neuroligins and neurexins link synaptic function to cognitive disease. Nature 455:903–911

    PubMed Central  Article  PubMed  Google Scholar 

  27. 27.

    Tsigelny I, Shindyalov IN, Bourne PE, Sudhof TC, Taylor P (2000) Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations. Protein Sci 9:180–185

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  28. 28.

    Nguyen T, Sudhof TC (1997) Binding properties of neuroligin 1 and neurexin 1 beta reveal function as heterophilic cell adhesion molecules. J Biol Chem 272:26032–26039

    CAS  Article  PubMed  Google Scholar 

Download references


We thank the patients and their families for agreeing to participate in this study and special teachers whose participation made this project possible. We also thank Cong Wang and Haoying Hao for sequencing, Jiada Li for manuscript revision. We were appreciated for the help and advices of our colleagues. This study was supported by the National Basic Research Program 973 of China (Grant No. 2012CB 517902, 2010 CB 529601) and the National Natural Science Foundation of China (Grant No. 81330027, 81161120544, 31301023).

Conflict of interest

The authors state no competing interests.

Author information



Corresponding authors

Correspondence to Kun Xia or Zhengmao Hu.

Additional information

Xiaojuan Xu, Zhimin Xiong and Lusi Zhang  contributed equally to this study.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 91 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Xu, X., Xiong, Z., Zhang, L. et al. Variations analysis of NLGN3 and NLGN4X gene in Chinese autism patients. Mol Biol Rep 41, 4133–4140 (2014).

Download citation


  • Autism
  • Neuroligin
  • NLGN
  • Variation