De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females

Genetics in Medicine (2020)Cite this article

Abstract

Purpose

Hardikar syndrome (MIM 612726) is a rare multiple congenital anomaly syndrome characterized by facial clefting, pigmentary retinopathy, biliary anomalies, and intestinal malrotation, but with preserved cognition. Only four patients have been reported previously, and none had a molecular diagnosis. Our objective was to identify the genetic basis of Hardikar syndrome (HS) and expand the phenotypic spectrum of this disorder.

Methods

We performed exome sequencing on two previously reported and five unpublished female patients with a clinical diagnosis of HS. X-chromosome inactivation (XCI) studies were also performed.

Results

We report clinical features of HS with previously undescribed phenotypes, including a fatal unprovoked intracranial hemorrhage at age 21. We additionally report the discovery of de novo pathogenic nonsense and frameshift variants in MED12 in these seven individuals and evidence of extremely skewed XCI in all patients with informative testing.

Conclusion

Pathogenic missense variants in the X-chromosome gene MED12 have previously been associated with Opitz–Kaveggia syndrome, Lujan syndrome, Ohdo syndrome, and nonsyndromic intellectual disability, primarily in males. We propose a fifth, female-specific phenotype for MED12, and suggest that nonsense and frameshift loss-of-function MED12 variants in females cause HS. This expands the MED12-associated phenotype in females beyond intellectual disability.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

Rent or Buy

All prices are NET prices.

Fig. 1: Photos of Hardikar syndrome patients.
Fig. 2: Schematic representation of the MED12 gene (not to scale).

Data availability

All variants have been deposited into ClinVar, VCV000432691, VCV000280361, VCV000620451, VCV000520705.

References

  1. 1.

    Bourbon, H. M. et al. A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. Mol. Cell 14, 553–557 (2004).

    CAS  Article  Google Scholar 

  2. 2.

    Harper, T. M. & Taatjes, D. J. The complex structure and function of mediator. J. Biol. Chem. 293, 13778–13785 (2018).

    CAS  Article  Google Scholar 

  3. 3.

    Fant, C. B. & Taatjes, D. J. Regulatory functions of the mediator kinases CDK8 and CDK19. Transcription 10, 76–90 (2019).

    Article  Google Scholar 

  4. 4.

    Graham, J. M. & Schwartz, C. E. MED12 related disorders. Am. J. Med. Genet. A 161, 2734–2740 (2013).

    CAS  Article  Google Scholar 

  5. 5.

    Allen, B. L. & Taatjes, D. J. The mediator complex: a central integrator of transcription. Nat. Rev. Mol. Cell Biol. 16, 155–166 (2015).

    CAS  Article  Google Scholar 

  6. 6.

    Hsieh, T. H. S. et al. Mapping nucleosome resolution chromosome folding in yeast by micro-C. Cell 162, 108–119 (2015).

    CAS  Article  Google Scholar 

  7. 7.

    Schneider, M. et al. The nuclear pore-associated TREX-2 complex employs mediator to regulate gene expression. Cell 162, 1016–1028 (2015).

    CAS  Article  Google Scholar 

  8. 8.

    Tutter, A. V. et al. Role for Med12 in regulation of Nanog and Nanog target genes. J. Biol. Chem 284, 3709–3718 (2009).

    CAS  Article  Google Scholar 

  9. 9.

    Hong, S. K. et al. The zebrafish kohtalo/trap230 gene is required for the development of the brain, neural crest, and pronephric kidney. Proc. Natl Acad. Sci. USA 102, 18473–18478 (2005).

    CAS  Article  Google Scholar 

  10. 10.

    Shin, C. H. et al. Multiple roles for Med12 in vertebrate endoderm development. Dev. Biol. 317, 467–479 (2008).

    CAS  Article  Google Scholar 

  11. 11.

    Wu, S. Y., de Borsetti, N. H., Bain, E. J., Bulow, C. R. & Gamse, J. T. Mediator subunit 12 coordinates intrinsic and extrinsic control of epithalamic development. Dev. Biol. 385, 13–22 (2014).

    CAS  Article  Google Scholar 

  12. 12.

    Rocha, P. P., Scholze, M., Bleiß, W. & Schrewe, H. Med12 is essential for early mouse development and for canonical Wnt and Wnt/PCP signaling. Development 137, 2723–2731 (2010).

    CAS  Article  Google Scholar 

  13. 13.

    Yin, J. W. & Wang, G. The mediator complex: a master coordinator of transcription and cell lineage development. Development 141, 977–987 (2014).

    CAS  Article  Google Scholar 

  14. 14.

    Kim, S., Xu, X., Hecht, A. & Boyer, T. G. Mediator is a transducer of Wnt/β-catenin signaling. J. Biol. Chem. 281, 14066–14075 (2006).

    CAS  Article  Google Scholar 

  15. 15.

    Lesca, G. et al. Clinical and neurocognitive characterization of a family with a novel MED12 gene frameshift mutation. Am. J. Med. Genet. A 161, 3063–3071 (2013).

    CAS  Article  Google Scholar 

  16. 16.

    Bouazzi, H., Lesca, G., Trujillo, C., Alwasiyah, M. K. & Munnich, A. Nonsyndromic X-linked intellectual deficiency in three brothers with a novel MED12 missense mutation [c.5922G>T (p.Glu1974His)]. Clin. Case Reports 3, 604–609 (2015).

    Article  Google Scholar 

  17. 17.

    Charzewska, A. et al. The power of the mediator complex-expanding the genetic architecture and phenotypic spectrum of MED12 -related disorders. Clin. Genet. 94, 450–456 (2018).

    CAS  Article  Google Scholar 

  18. 18.

    Prontera, P. et al. A novel MED12 mutation: evidence for a fourth phenotype. Am. J. Med. Genet. A 170, 2377–2382 (2016).

    CAS  Article  Google Scholar 

  19. 19.

    Hardikar, W., Smith, A. L., Keith, C. G. & Chow, C. W. Multisystem obstruction with cholestasis, pigmentary retinopathy, and cleft palate: a new syndrome? Am. J. Med. Genet. 44, 13–17 (1992).

    CAS  Article  Google Scholar 

  20. 20.

    Cools, F. & Jaeken, J. Hardikar syndrome: A new syndrome with cleft lip/palate, pigmentary retinopathy and cholestasis. Am. J. Med. Genet. 71, 472–474 (1997).

    CAS  Article  Google Scholar 

  21. 21.

    Poley, J. R. & Proud, V. K. Hardikar syndrome: new features. Am. J. Med. Genet. A 146, 2473–2479 (2008).

    Article  Google Scholar 

  22. 22.

    Ryan, K. M. et al. Aortic coarctation and carotid artery aneurysm in a patient with hardikar syndrome: cardiovascular implications for affected individuals. Am. J. Med. Genet. A 170, 482–486 (2016).

    Article  Google Scholar 

  23. 23.

    Nydegger, A., Van Dyck, M., Fisher, R. A., Jaeken, J. & Hardikar, W. Hardikar syndrome: long term outcome of a rare genetic disorder. Am. J. Med. Genet. A 146, 2468–2472 (2008).

    Article  Google Scholar 

  24. 24.

    Kurosaki, T., Popp, M. W. & Maquat, L. E. Quality and quantity control of gene expression by nonsense-mediated mRNA decay. Nat. Rev. Mol. Cell. Biol. 20, 406–420 (2019).

    CAS  Article  Google Scholar 

  25. 25.

    Schwartz, C. E. et al. The original Lujan syndrome family has a novel missense mutation (p.N1007S) in the MED12 gene. J. Med. Genet. 44, 472–477 (2007).

    CAS  Article  Google Scholar 

  26. 26.

    Clark, R. D. et al. FG syndrome, an X-linked multiple congenital anomaly syndrome: the clinical phenotype and an algorithm for diagnostic testing. Genet. Med. 11, 769–775 (2009).

    Article  Google Scholar 

  27. 27.

    Rump, P. et al. A novel mutation in MED12 causes FG syndrome (Opitz-Kaveggia syndrome). Clin. Genet. 79, 183–188 (2011).

    CAS  Article  Google Scholar 

  28. 28.

    Lyons MJ. MED12-Related Disorders. 2008 Jun 23 [updated 2016 Aug 11]. In GeneReviews® [Internet]. (eds Adam, M. P. et al.) (Seattle (WA): University of Washington, Seattle, 1993–2020).

  29. 29.

    Murakami, H., Enomoto, Y., Tsurusaki, Y., Sugio, Y. & Kurosawa, K. A female patient with X‐linked Ohdo syndrome of the Maat‐Kievit‐Brunner phenotype caused by a novel variant of MED12. Congenit. Anom. 60, 91–93 (2019).

    Article  Google Scholar 

  30. 30.

    Fieremans, N. et al. Identification of Intellectual disability genes in female patients with a skewed X-inactivation pattern. Hum. Mutat. 37, 804–811 (2016).

    CAS  Article  Google Scholar 

  31. 31.

    Wang, C. et al. MED12-related disease in a chinese girl: clinical characteristics and underlying mechanism. Front Genet 11, 129 (2020).

    Article  Google Scholar 

  32. 32.

    Kosmicki, J. A. et al. Refining the role of de novo protein-truncating variants in neurodevelopmental disorders by using population reference samples. Nat. Genet. 49, 504–510 (2017).

    CAS  Article  Google Scholar 

  33. 33.

    Hoffbuhr, K. et al. MeCP2 mutations in children with and without the phenotype of Rett syndrome. Neurology 56, 1486–1495 (2001).

    CAS  Article  Google Scholar 

  34. 34.

    Zito, A. et al. Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age. Nat. Commun. 10, 5339 (2019).

    Article  Google Scholar 

  35. 35.

    Donnio, L. M. et al. MED12-related XLID disorders are dose-dependent of immediate early genes (IEGs) expression. Hum. Mol. Genet. 26, 2062–2075 (2017).

    CAS  Article  Google Scholar 

  36. 36.

    Srivastava, S. et al. Dysregulations of sonic hedgehog signaling in MED12‐related X‐linked intellectual disability disorders. Mol. Genet. Genomic Med. 7, e00569 (2019).

    Article  Google Scholar 

  37. 37.

    Ejarque, I. et al. Is Hardikar syndrome distinct from Kabuki (Niikawa—Kuroki) syndrome? Clin. Genet. 80, 493–496 (2011).

    CAS  Article  Google Scholar 

  38. 38.

    Cheng, D. et al. CARM1 methylates MED12 to regulate its RNA-binding ability. Life Sci. Alliance 1, e201800117 (2018).

    Article  Google Scholar 

  39. 39.

    Aranda-Orgilles, B. et al. MED12 regulates HSC-specific enhancers independently of mediator kinase activity to control hematopoiesis. Cell Stem Cell 19, 784–799 (2016).

    CAS  Article  Google Scholar 

  40. 40.

    Verhagen, J. M. A., Oostdijk, W., Terwisscha van Scheltinga, C. E. J., Schalij-Delfos, N. E. & van Bever, Y. An unusual presentation of Kabuki syndrome: clinical overlap with CHARGE syndrome. Eur. J. Med. Genet. 57, 510–512 (2014).

    Article  Google Scholar 

  41. 41.

    Schulz Y. et al. CHARGE and Kabuki syndromes: a phenotypic and molecular link. Hum. Mol. Genet. 23, 4396–4405 (2014).

Download references

Acknowledgements

We thank all the patients and families who participated in this study. There are no funders to acknowledge.

Author information

Author notes

  1. These authors contributed equally: Dong Li, Alanna Strong.

Affiliations

  1. Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Dong Li PhD, Alanna Strong MD PhD, Kaitlyn M. Shen BS, Tiancheng Wang BS, Hakon Hakonarson MD PhD & Elizabeth Bhoj MD PhD

  2. Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA

    Alanna Strong MD PhD, Elaine Zackai MD, Hakon Hakonarson MD PhD & Elizabeth Bhoj MD PhD

  3. University Hospitals and University of Leuven, Metabolic Center, Leuven, Belgium

    David Cassiman MD PhD & Jaak Jaeken MD PhD

  4. University Hospitals and University of Leuven, Pediatric Nephrology, Leuven, Belgium

    Maria Van Dyck MD

  5. Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    Natalia Duarte Linhares PhD

  6. CENTRARE–Centro de Referência em fendas orofaciais, Fundação Benjamin Guimarães–Hospital da Baleia, Belo Horizonte, Brazil

    Eugenia Ribeiro Valadares MD PhD

  7. Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil

    Sergio D. J. Pena MD PhD

  8. Laboratório Gene–Núcleo de Genética Médica, Belo Horizonte, Brazil

    Sergio D. J. Pena MD PhD

  9. Division of Medical Genetics and Metabolism, Children’s Hospital of The King’s Daughters, Norfolk, VA, USA

    Samantha Vergano MD

  10. Department of Pediatrics, Eastern Virginia Medical School, Norfolk, VA, USA

    Samantha Vergano MD

  11. Division of Genetics, Seattle Children’s Hospital, Seattle, WA, USA

    Anne Hing MD & Penny Chow MS LGC

  12. Department of Genetics, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA

    Arupa Ganguly PhD

  13. Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany

    Tasja Scholz MD & Tatjana Bierhals MD

  14. Department of Neonatology and Pediatric Intensive Care Medicine, University Children’s Hospital, University Medical Center Hamburg Eppendorf, Hamburg, Germany

    Deindl Philipp MD

Authors
  1. Dong Li PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alanna Strong MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kaitlyn M. Shen BS
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. David Cassiman MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Maria Van Dyck MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Natalia Duarte Linhares PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Eugenia Ribeiro Valadares MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Tiancheng Wang BS
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Sergio D. J. Pena MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Jaak Jaeken MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Samantha Vergano MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Elaine Zackai MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Anne Hing MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Penny Chow MS LGC
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Arupa Ganguly PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Tasja Scholz MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Tatjana Bierhals MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Deindl Philipp MD
    View author publications

    You can also search for this author in PubMed Google Scholar

  19. Hakon Hakonarson MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

  20. Elizabeth Bhoj MD PhD
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Conceptualization: E.B., D.L., H.H.; Data curation: D.L; Formal Analysis: D.L; Investigation: R.L., D.C., M.V., N.D.L., E.R.V, T.W., S.P., J.J., S.V., E.Z., A.H., P.C., A.G., T.S., T.B., D.P.; Resources: H.H.; Visualization: A.S, D.L; Writing – original draft: A.S.,K.S., D.L; Writing – review & editing: E.B., H.H.

Corresponding author

Correspondence to Elizabeth Bhoj MD PhD.

Ethics declarations

COMPETING INTERESTS

The authors declare no competing interests.

Ethics Declaration

All individuals’ families from the different institutions agreed to participate in this study and signed appropriate consent forms. The Institutional Review Board of the Children’s Hospital of Philadelphia approved this study. Permission for clinical photographs was given separately.

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

Li, D., Strong, A., Shen, K.M. et al. De novo loss-of-function variants in X-linked MED12 are associated with Hardikar syndrome in females. Genet Med (2020). https://doi.org/10.1038/s41436-020-01031-7

Download citation

Search

Quick links