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Developmental defects
Original research
A novel homozygous variant in TRAPPC2L results in a neurodevelopmental disorder and disrupts TRAPP complex function
  1. Noraldin Al-deri1,
  2. Volkan Okur2,
  3. Priyanka Ahimaz2,
  4. Miroslav Milev1,
  5. Zaheer Valivullah3,
  6. Jacob Hagen4,
  7. Yufeng Sheng4,
  8. Wendy Chung2,5,
  9. Michael Sacher1,6,
  10. Mythily Ganapathi7
  1. 1 Department of Biology, Concordia University, Montreal, Quebec, Canada
  2. 2 Department of Pediatrics, Columbia University Medical Center, New York, New York, USA
  3. 3 Center for Mendelian Genomics, Broad Institute Harvard, Cambridge, Massachusetts, USA
  4. 4 Department of Biomedical Sciences, Columbia University Medical Center, New York, New York, USA
  5. 5 Department of Medicine, Columbia University Medical Center, New York, New York, USA
  6. 6 Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
  7. 7 Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
  1. Correspondence to Dr. Mythily Ganapathi, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA; mg3560{at}cumc.columbia.edu; Dr. Michael Sacher, Department of Biology, Concordia University, Montreal, Quebec, Canada; michael.sacher{at}concordia.ca

Abstract

Background Next-generation sequencing has facilitated the diagnosis of neurodevelopmental disorders with variable and non-specific clinical findings. Recently, a homozygous missense p.(Asp37Tyr) variant in TRAPPC2L, a core subunit of TRAPP complexes which function as tethering factors during membrane trafficking, was reported in two unrelated individuals with neurodevelopmental delay, post-infectious encephalopathy-associated developmental arrest, tetraplegia and accompanying rhabdomyolysis.

Methods We performed whole genome sequencing on members of an Ashkenazi Jewish pedigree to identify the underlying genetic aetiology of global developmental delay/intellectual disability in three affected siblings. To assess the effect of the identified TRAPPC2L variant, we performed biochemical and cell biological functional studies on the TRAPPC2L protein.

Results A rare homozygous predicted deleterious missense variant, p.(Ala2Gly), in TRAPPC2L was identified in the affected siblings and it segregated with the neurodevelopmental phenotype within the family. Using a yeast two-hybrid assay and in vitro binding, we demonstrate that the p.(Ala2Gly) variant, but not the p.(Asp37Tyr) variant, disrupted the interaction between TRAPPC2L and another core TRAPP protein, TRAPPC6a. Size exclusion chromatography suggested that this variant affects the assembly of TRAPP complexes. Employing two different membrane trafficking assays using fibroblasts from one of the affected siblings, we found a delay in traffic into and out of the Golgi. Similar to the p.(Asp37Tyr) variant, the p.(Ala2Gly) variant resulted in an increase in the levels of active RAB11.

Conclusion Our data fill in a gap in the knowledge of TRAPP architecture with TRAPPC2L interacting with TRAPPC6a, positioning it as a putative adaptor for other TRAPP subunits. Collectively, our findings support the pathogenicity of the TRAPPC2L p.(Ala2Gly) variant.

  • genetics, medical

Data availability statement

All data relevant to the study are included in the article or uploaded as online supplementary information.

https://doi.org/10.1136/jmedgenet-2020-107016

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    Data availability statement

    All data relevant to the study are included in the article or uploaded as online supplementary information.

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    Footnotes

    • MS and MG are joint senior authors.

    • Correction notice The article has been corrected since it was published Online first. The link to online supplemental figures 1A and 1B has been corrected.

    • Contributors NA-d and MM performed the experiments, interpreted the data and edited the manuscript. VO analysed the data, drafted and critically reviewed the manuscript. PA provided the clinical data. ZV analysed the data. JH and YS provided and interpreted the haplotype data. WC conceived of the study, provided clinical data, analysed the data and critically reviewed the manuscript. MG analysed and interpreted the data, drafted, critically reviewed and edited the manuscript. MS designed the study, interpreted the data, and wrote and edited the manuscript.

    • Funding This work was supported by funding from the JPB Foundation, SFARI to WC, the Center for Mendelian Genomics (NHGRI HG009141), and by the Canadian Institutes of Health Research and the Natural Sciences and Engineering Research Council of Canada to MS. Sequencing and analysis were provided by the Broad Institute of MIT and Harvard Center for Mendelian Genomics (Broad CMG) and was funded by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung and Blood Institute grant UM1 HG008900 and in part by National Human Genome Research Institute grant R01 HG009141.

    • Competing interests None declared.

    • Provenance and peer review Not commissioned; externally peer reviewed.