Recessive variants in ZNF142 cause a complex neurodevelopmental disorder with intellectual disability, speech impairment, seizures, and dystonia

Abstract

Purpose

The purpose of this study was to expand the genetic architecture of neurodevelopmental disorders, and to characterize the clinical features of a novel cohort of affected individuals with variants in ZNF142, a C2H2 domain-containing transcription factor.

Methods

Four independent research centers used exome sequencing to elucidate the genetic basis of neurodevelopmental phenotypes in four unrelated families. Following bioinformatic filtering, query of control data sets, and secondary variant confirmation, we aggregated findings using an online data sharing platform. We performed in-depth clinical phenotyping in all affected individuals.

Results

We identified seven affected females in four pedigrees with likely pathogenic variants in ZNF142 that segregate with recessive disease. Affected cases in three families harbor either nonsense or frameshifting likely pathogenic variants predicted to undergo nonsense mediated decay. One additional trio bears ultrarare missense variants in conserved regions of ZNF142 that are predicted to be damaging to protein function. We performed clinical comparisons across our cohort and noted consistent presence of intellectual disability and speech impairment, with variable manifestation of seizures, tremor, and dystonia.

Conclusion

Our aggregate data support a role for ZNF142 in nervous system development and add to the emergent list of zinc finger proteins that contribute to neurocognitive disorders.

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Acknowledgements

We are grateful to the patient families for their engagement and support of our research. We thank J. Willer for assistance with ES library prep (family C). This work was supported by grants from the National Institutes of Health (P50DK096415 to N.K. and MH106826 to E.E.D.). This study was funded in part by the Czech Science Foundation (GACR16-13323S) as well as in-house institutional funding from Technische Universität München, Munich, Germany; Helmholtz Zentrum München, Munich, Germany; and Charles University, Prague, Czech Republic (PROGRES Q27). This study was also supported by the Slovak Grant and Development Agency under contract APVV-14-0415 to M.S., V.H., and Z.G. Additionally, K.K. was funded by an International Research Support Initiative Program fellowship from the Higher Education Commission of Pakistan. M.Z. was supported by an internal research program at Helmholtz Center Munich, Germany (Physician Scientists for Groundbreaking Projects). D.D.L. was supported by DFG grant LA 3830/1-1. This work was also supported by Australian National Health & Medical Research Council (NHMRC) Project (ID: 1127144) and Centre of Research Excellence (ID: 1116976) grants to A.T.M., and the Victorian Government’s Operational Infrastructure Support Program and NHMRC Independent Research Institute Infrastructure Support Scheme (NHMRC IRIISS) to M.B. A.T.M. was supported by NHMRC Practitioner Fellowship 1105008. M.B. was supported by an NHMRC program grant (ID: 1054618) and NHMRC Senior Research Fellowship (ID: 1102971). M.S.H. was supported by an NHMRC Career Development Fellowship (ID:1063799).

Author information

Correspondence to Nicholas Katsanis PhD or Juliane Winkelmann MD.

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Disclosure

N.K. is a paid consultant for and holds significant stock in Rescindo Therapeutics, Inc. The other authors declare no conflicts of interest.

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These senior co-authors contributed equally: Nicholas Katsanis and Juliane Winkelmann.

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Keywords

  • homozygosity mapping
  • developmental delay
  • ataxia
  • dolichocephaly
  • childhood apraxia of speech