J Med Genet 46:389-398 doi:10.1136/jmg.2008.063818
  • Original article

Clinical spectrum of SIX3-associated mutations in holoprosencephaly: correlation between genotype, phenotype and function

  1. F Lacbawan1,2,
  2. B D Solomon1,
  3. E Roessler1,
  4. K El-Jaick1,
  5. S Domené1,
  6. J I Vélez1,
  7. N Zhou1,
  8. D Hadley1,
  9. J Z Balog1,
  10. R Long1,
  11. A Fryer3,
  12. W Smith4,
  13. S Omar5,
  14. S D McLean6,
  15. K Clarkson7,
  16. A Lichty7,
  17. N J Clegg8,
  18. M R Delgado8,
  19. E Levey9,
  20. E Stashinko9,
  21. L Potocki10,
  22. M I VanAllen11,
  23. J Clayton-Smith12,
  24. D Donnai12,
  25. D W Bianchi13,
  26. P B Juliusson14,
  27. P R Njølstad14,15,
  28. H G Brunner16,
  29. J C Carey17,
  30. U Hehr18,
  31. J Müsebeck19,
  32. P F Wieacker20,
  33. A Postra21,
  34. R C M Hennekam22,
  35. M-J H van den Boogaard23,
  36. A van Haeringen24,
  37. A Paulussen25,
  38. J Herbergs25,
  39. C T R M Schrander-Stumpel25,
  40. A R Janecke26,
  41. D Chitayat27,
  42. J Hahn28,
  43. D M McDonald-McGinn29,
  44. E H Zackai29,
  45. W B Dobyns30,
  46. M Muenke1
  1. 1
    Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
  2. 2
    Department of Pathology, State University of New York-Downstate Medical Center, Brooklyn, NY, USA
  3. 3
    Department of Clinical Genetics, Royal Liverpool Children’s Hospital (Alder Hey), Liverpool, UK
  4. 4
    Department of Genetics, Maine Medical Center, Portland, ME, USA
  5. 5
    Department of Neonatalogy, College of Human Medicine, Michigan State University, MI, USA
  6. 6
    Departments of Pediatrics and Genetics, San Antonio Military Medical Center, San Antonio, TX, USA
  7. 7
    Department of Clinical Genetics, Greenwood Genetic Center, Columbia, SC, USA
  8. 8
    Department of Neurology, Texas Scottish Rite Hospital for Children, University of Texas Southwestern Medical Center, Dallas, TX, USA
  9. 9
    Kennedy Krieger Institute, Johns Hopkins University, Baltimore, MD, USA
  10. 10
    Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children’s Hospital, Houston, TX, USA
  11. 11
    Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
  12. 12
    Academic Department of Medical Genetics and Regional Genetic Services, St Mary’s Hospital, University of Manchester, Manchester, UK
  13. 13
    Division of Genetics, Department of Pediatrics, Tufts University School of Medicine, Boston, MA, USA
  14. 14
    Department of Paediatrics, Haukeland University Hospital, Bergen, Norway
  15. 15
    Department of Clinical Medicine, University of Bergen, Bergen, Norway
  16. 16
    Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, Netherlands
  17. 17
    Division of Medical Genetics, University of Utah Medical Center, Salt Lake City, UT, USA
  18. 18
    Department of Human Genetics, University of Regensburg, Regensburg, Germany
  19. 19
    Center for Human Genetics, University of Bremen, Bremen, Germany
  20. 20
    Institute of Human Genetics, University of Munster, Munster, Germany
  21. 21
    Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
  22. 22
    Institute of Child Health, Great Ormond Street Hospital for Children, London, UK
  23. 23
    Department of Medical Genetics, University Medical Centre Utrecht, Netherlands
  24. 24
    Department of Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands
  25. 25
    Department of Clinical Genetics, Academic Hospital Maastricht, Maastricht, Netherlands
  26. 26
    Division of Clinical Genetics, Innsbruck Medical University, Innsbruck, Austria
  27. 27
    Prenatal Diagnostics and Medical Genetics, Mt. Sinai Hospital, Toronto, ON, Canada
  28. 28
    Department of Neurology, Stanford University School of Medicine, Palo Alto, CA, USA
  29. 29
    Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
  30. 30
    Departments of Human Genetics, Neurology and Pediatrics, The University of Chicago, Chicago, IL, USA
  1. Maximilian Muenke, MD, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, 35 Convent Drive, MSC 3717, Building 35, Room 1B-203, Bethesda, MD 20892-3717; mamuenke{at}
  • Received 31 October 2008
  • Revised 23 December 2008
  • Accepted 21 January 2009
  • Published Online First 2 April 2009


Background: Holoprosencephaly (HPE) is the most common structural malformation of the human forebrain. There are several important HPE mutational target genes, including the transcription factor SIX3, which encodes an early regulator of Shh, Wnt, Bmp and Nodal signalling expressed in the developing forebrain and eyes of all vertebrates.

Objective: To characterise genetic and clinical findings in patients with SIX3 mutations.

Methods: Patients with HPE and their family members were tested for mutations in HPE-associated genes and the genetic and clinical findings, including those for additional cases found in the literature, were analysed. The results were correlated with a mutation-specific functional assay in zebrafish.

Results: In a cohort of patients (n = 800) with HPE, SIX3 mutations were found in 4.7% of probands and additional cases were found through testing of relatives. In total, 138 cases of HPE were identified, 59 of whom had not previously been clinically presented. Mutations in SIX3 result in more severe HPE than in other cases of non-chromosomal, non-syndromic HPE. An over-representation of severe HPE was found in patients whose mutations confer greater loss of function, as measured by the functional zebrafish assay. The gender ratio in this combined set of patients was 1.5:1 (F:M) and maternal inheritance was almost twice as common as paternal. About 14% of SIX3 mutations in probands occur de novo. There is a wide intrafamilial clinical range of features and classical penetrance is estimated to be at least 62%.

Conclusions: Our data suggest that SIX3 mutations result in relatively severe HPE and that there is a genotype–phenotype correlation, as shown by functional studies using animal models.


  • Additional data are published online only at

  • For numbered affiliations see end of article

  • The first two authors contributed equally to this work.

  • Funding: This research was supported by the Division of Intramural Research, National Human Genome Research Institute, National Institutes of Health, Department of Health and Human Services, USA

  • Competing interests: There are no competing interests.

  • Patient consent: Obtained.