TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila

Am J Hum Genet. 2021 Sep 2;108(9):1669-1691. doi: 10.1016/j.ajhg.2021.06.019. Epub 2021 Jul 26.


Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities.

Keywords: Drosophila; Importin-3; Karyopherin-β2b; TNPO1; TNPO2; Transportin; global developmental delays; intellectual disability; nucleocytoplasmic shuttling; rare disease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Amino Acid Sequence
  • Animals
  • Developmental Disabilities / genetics*
  • Developmental Disabilities / metabolism
  • Developmental Disabilities / pathology
  • Drosophila Proteins / antagonists & inhibitors
  • Drosophila Proteins / genetics*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / genetics
  • Drosophila melanogaster / growth & development
  • Drosophila melanogaster / metabolism
  • Eye Diseases, Hereditary / genetics*
  • Eye Diseases, Hereditary / metabolism
  • Eye Diseases, Hereditary / pathology
  • Female
  • Gene Dosage
  • Gene Expression Regulation, Developmental
  • Genome, Human
  • Humans
  • Infant
  • Infant, Newborn
  • Intellectual Disability / genetics*
  • Intellectual Disability / metabolism
  • Intellectual Disability / pathology
  • Karyopherins / antagonists & inhibitors
  • Karyopherins / genetics*
  • Karyopherins / metabolism
  • Male
  • Musculoskeletal Abnormalities / genetics*
  • Musculoskeletal Abnormalities / metabolism
  • Musculoskeletal Abnormalities / pathology
  • Mutation
  • Neurons / metabolism
  • Neurons / pathology
  • RNA, Small Interfering / genetics
  • RNA, Small Interfering / metabolism
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Whole Genome Sequencing
  • beta Karyopherins / genetics*
  • beta Karyopherins / metabolism
  • ran GTP-Binding Protein / genetics*
  • ran GTP-Binding Protein / metabolism


  • Drosophila Proteins
  • Karyopherins
  • RNA, Small Interfering
  • TNPO2 protein, human
  • Tnpo protein, Drosophila
  • beta Karyopherins
  • ran GTP-Binding Protein