Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Biallelic UBE4A loss-of-function variants cause intellectual disability and global developmental delay



To identify novel genes associated with intellectual disability (ID) in four unrelated families.


Here, through exome sequencing and international collaboration, we report eight individuals from four unrelated families of diverse geographic origin with biallelic loss-of-function variants in UBE4A.


Eight evaluated individuals presented with syndromic intellectual disability and global developmental delay. Other clinical features included hypotonia, short stature, seizures, and behavior disorder. Characteristic features were appreciated in some individuals but not all; in some cases, features became more apparent with age. We demonstrated that UBE4A loss-of-function variants reduced RNA expression and protein levels in clinical samples. Mice generated to mimic patient-specific Ube4a loss-of-function variant exhibited muscular and neurological/behavioral abnormalities, some of which are suggestive of the clinical abnormalities seen in the affected individuals.


These data indicate that biallelic loss-of-function variants in UBE4A cause a novel intellectual disability syndrome, suggesting that UBE4A enzyme activity is required for normal development and neurological function.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Family pedigrees, clinical pictures and UBE4A pathogenic variants of individuals from four unrelated families.
Fig. 2: Gene and protein expression.
Fig. 3: Ube4aC425Ffs* mice have mild cataracts.
Fig. 4: Phenotype assessment tests conducted on homozygous Ube4aC425Ffs* and wild-type (WT) mice.

Data availability

Data and materials are available upon request.


  1. 1.

    Schalock, R. L., Borthwick-Duffy, S. A. & Bradley, M. et al. Intellectual Disability: Definition, Classification, and Systems of Supports 11th edn. (American Association on Intellectual and Developmental Disabilities, Washington DC, 2010).

  2. 2.

    Maulik, P. K., Mascarenhas, M. N., Mathers, C. D., Dua, T. & Saxena, S. Prevalence of intellectual disability: a meta-analysis of population-based studies. Res. Dev. Disabil. 32, 419–436 (2011).

    Article  Google Scholar 

  3. 3.

    Kochinke, K. et al. Systematic phenomics analysis deconvolutes genes mutated in intellectual disability into biologically coherent modules. Am. J. Hum. Genet. 98, 149–164 (2016).

    CAS  Article  Google Scholar 

  4. 4.

    Anazi, S. et al. Expanding the genetic heterogeneity of intellectual disability. Hum. Genet. 136, 1419–1429 (2017).

    Article  Google Scholar 

  5. 5.

    Anazi, S. et al. Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield. Mol. Psychiatry 22, 615–624 (2017).

    CAS  Article  Google Scholar 

  6. 6.

    Monies, D. et al. Lessons learned from large-scale, first-tier clinical exome sequencing in a highly consanguineous population. Am. J. Hum. Genet. 104, 1182–1201 (2019).

    CAS  Article  Google Scholar 

  7. 7.

    Hershko, A. & Ciechanover, A. The ubiquitin system for protein degradation. Annu. Rev. Biochem. 61, 761–807 (1992).

    CAS  Article  Google Scholar 

  8. 8.

    Ravid, T. & Hochstrasser, M. Diversity of degradation signals in the ubiquitin-proteasome system. Nat. Rev. Mol. Cell. Biol. 9, 679–690 (2008).

    CAS  Article  Google Scholar 

  9. 9.

    Koegl, M., Hoppe, T., Schlenker, S., Ulrich, H. D., Mayer, T. U. & Jentsch, S. A novel ubiquitination factor, E4, is involved in multiubiquitin chain assembly. Cell. 96, 635–644 (1999).

    CAS  Article  Google Scholar 

  10. 10.

    Tu, D., Li, W., Ye, Y. & Brunger, A. T. Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. Proc. Natl. Acad. Sci. U S A 104, 15599–15606 (2007).

    CAS  Article  Google Scholar 

  11. 11.

    Hellerschmied, D. et al. UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins. Nat Commun 9, 484 (2018).

    Article  Google Scholar 

  12. 12.

    Kishino, T., Lalande, M. & Wagstaff, J. UBE3A/E6-AP mutations cause Angelman syndrome [published correction appears in Nat Genet 1997 Apr;15(4):411]. Nat. Genet. 15, 70–73 (1997).

    CAS  Article  Google Scholar 

  13. 13.

    Nascimento, R. M., Otto, P. A., de Brouwer, A. P. & Vianna-Morgante, A. M. UBE2A, which encodes a ubiquitin-conjugating enzyme, is mutated in a novel X-linked mental retardation syndrome. Am. J. Hum. Genet. 79, 549–555 (2006).

    CAS  Article  Google Scholar 

  14. 14.

    Basel-Vanagaite, L. et al. Deficiency for the ubiquitin ligase UBE3B in a blepharophimosis-ptosis-intellectual-disability syndrome. Am. J. Hum. Genet. 91, 998–1010 (2012).

    CAS  Article  Google Scholar 

  15. 15.

    Frints, S. G. M. et al. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol. Psychiatry 24, 1748–1768 (2019).

    CAS  Article  Google Scholar 

  16. 16.

    Sobreira, N., Schiettecatte, F., Valle, D. & Hamosh, A. GeneMatcher: a matching tool for connecting investigators with an interest in the same gene. Hum. Mutat. 36, 928–930 (2015).

    Article  Google Scholar 

  17. 17.

    Schmittgen, T. D. & Livak, K. J. Analyzing real-time PCR data by the comparative C(T) method. Nat. Protoc. 3, 1101–1108 (2008).

    CAS  Article  Google Scholar 

  18. 18.

    Labun, K., Montague, T. G., Krause, M., Torres Cleuren, Y. N., Tjeldnes, H. & Valen, E. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 47, W171–W174 (2019).

    CAS  Article  Google Scholar 

  19. 19.

    Richardson, C. D., Ray, G. J., DeWitt, M. A., Curie, G. L. & Corn, J. E. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat. Biotechnol. 34, 339–344 (2016).

    CAS  Article  Google Scholar 

  20. 20.

    Modzelewski, A. J., Chen, S., Willis, B. J., Lloyd, K. C. K., Wood, J. A. & He, L. Efficient mouse genome engineering by CRISPR-EZ technology. Nat. Protoc. 13, 1253–1274 (2018).

    CAS  Article  Google Scholar 

  21. 21.

    Tesson, L., Heslan, J. M., Ménoret, S. & Anegon, I. Rapid and accurate determination of zygosity in transgenic animals by real-time quantitative PCR. Transgenic Res. 11, 43–48 (2002).

    CAS  Article  Google Scholar 

  22. 22.

    Böhm, S., Lamberti, G., Fernández-Sáiz, V., Stapf, C. & Buchberger, A. Cellular functions of Ufd2 and Ufd3 in proteasomal protein degradation depend on Cdc48 binding. Mol. Cell. Biol. 31, 1528–1539 (2011).

    Article  Google Scholar 

  23. 23.

    Baranes-Bachar, K. et al. The ubiquitin E3/E4 ligase UBE4A adjusts protein ubiquitylation and accumulation at sites of DNA damage, facilitating double-strand break repair. Mol. Cell. 69, 866–878 (2018).

    CAS  Article  Google Scholar 

  24. 24.

    Carén, H., Holmstrand, A., Sjöberg, R. M. & Martinsson, T. The two human homologues of yeast UFD2 ubiquitination factor, UBE4A and UBE4B, are located in common neuroblastoma deletion regions and are subject to mutations in tumours. Eur. J. Cancer 42, 381–387 (2006).

    Article  Google Scholar 

  25. 25.

    Zhang, M. P., Zhang, W. S., Tan, J., Zhao, M. H., Lian, L. J. & Cai, J. Poly r(C) binding protein (PCBP) 1 expression is regulated by the E3 ligase UBE4A in thyroid carcinoma. Biosci. Rep. 37, BSR20170114 (2017).

    CAS  Article  Google Scholar 

  26. 26.

    Naudin, C. et al. SLAP displays tumour suppressor functions in colorectal cancer via destabilization of the SRC substrate EPHA2. Nat. Commun. 5, 3159 (2014).

    Article  Google Scholar 

Download references


We thank the patients and families for their support and participation. This study was supported by a grant from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) (CEPID number 2013/08028-1, 2014/15982-6) and by a grant from the National Institutes of Health (NIH) Office of the Director (U42OD012210). U.S.M. was fellow of FAPESP (2016/14517-3). We also thank Euna Koo for the image in Figure S3.

Author information




Conceptualization: U.S.M., D.B., F.K., H.M.B. Funding acquisition: U.S.M., M.Z., F.K., H.M.B. Methodology: U.S.M., D.B., J.A.B., K.D., J.P.K., F.K., H.M.B. Project administration: U.S.M., F.K., H.M.B. Resources: K.C.K.L., M.Z., C.F.M.M., E.S., N.D.D., F.S.A., F.K., H.M.B. Validation: B.W., L.B., B.C.L., D.J.M., F.G., F.d.S.L., D.O., F.P.M., M.T.W., A.J., M.H., H.S.A., A.C. Visualization: U.S.M., D.B., A.M., L.L. Writing—original draft: U.S.M, D.B., F.K., H.M.B. Writing—review & editing: U.S.M, D.B., F.K., H.M.B.

Corresponding authors

Correspondence to Uirá Souto Melo PhD or Heather M. Byers MD.

Ethics declarations

Ethics declaration

Studies were independently approved by the review boards of the participating institutions and performed according to local laws: family A: University of Sao Paulo CAAE 77680117.0.0000.5464; family B: Stanford University, IRB 28362; family C: King Faisal Specialist Hospital and Research Centre (KFSHRC) RAC 2121053; family D: German Gene Diagnostic Act (Gendiagnostikgesetz), EK 273072018. Written informed consent was obtained from parents or legal guardians to participate in these studies, giving permission to use patients’ (1) DNA samples for genomic sequencing, (2) blood or skin fibroblasts for establishing cell lines, and (3) photos for research publications and presentations. Mouse Model: All animal use was conducted in accordance with the Animal Welfare Act and the 2013 American Veterinary Medical Association (AVMA) Guidelines on Euthanasia. All studies were done consistent with the Institute for Laboratory Animal Research (ILAR) 8th Revision to the Guide for the Care and Use of Laboratory Animals and in compliance with and with prior approval from the University of California–Davis institutional animal care and use committee (IACUC).

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Melo, U.S., Bonner, D., Kent Lloyd, K.C. et al. Biallelic UBE4A loss-of-function variants cause intellectual disability and global developmental delay. Genet Med 23, 661–668 (2021).

Download citation


Quick links