Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder

Marije Meuwissen, Aline Verstraeten, Emmanuelle Ranza, Justyna Iwaszkiewicz, Maaike Bastiaansen, Ligia Mateiu, Merlijn Nemegeer, Josephina A.N. Meester, Alexandra Afenjar, Michelle Amaral, Diana Ballhausen, Sarah Barnett, Magalie Barth, Bob Asselbergh, Katrien Spaas, Bavo Heeman, Jennifer Bassetti, Patrick Blackburn, Marie Schaer, Xavier BlancVincent Zoete, Kari Casas, Thomas Courtin, Diane Doummar, Frédéric Guerry, Boris Keren, John Pappas, Rachel Rabin, Amber Begtrup, Marwan Shinawi, Anneke T. Vulto-van Silfhout, Tjitske Kleefstra, Matias Wagner, Alban Ziegler, Elise Schaefer, Benedicte Gerard, Charlotte I. De Bie, Sjoerd J.B. Holwerda, Mary Alice Abbot, Stylianos E. Antonarakis, Bart Loeys

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


Purpose: CTR9 is a subunit of the PAF1 complex (PAF1C) that plays a crucial role in transcription regulation by binding CTR9 to RNA polymerase II. It is involved in transcription-coupled histone modification through promoting H3K4 and H3K36 methylation. We describe the clinical and molecular studies in 13 probands, harboring likely pathogenic CTR9 missense variants, collected through GeneMatcher. Methods: Exome sequencing was performed in all individuals. CTR9 variants were assessed through 3-dimensional modeling of the activated human transcription complex Pol II-DSIF-PAF-SPT6 and the PAF1/CTR9 complex. H3K4/H3K36 methylation analysis, mitophagy assessment based on tetramethylrhodamine ethyl ester perchlorate immunofluorescence, and RNA-sequencing in skin fibroblasts from 4 patients was performed. Results: Common clinical findings were variable degrees of intellectual disability, hypotonia, joint hyperlaxity, speech delay, coordination problems, tremor, and autism spectrum disorder. Mild dysmorphism and cardiac anomalies were less frequent. For 11 CTR9 variants, de novo occurrence was shown. Three-dimensional modeling predicted a likely disruptive effect of the variants on local CTR9 structure and protein interaction. Additional studies in fibroblasts did not unveil the downstream functional consequences of the identified variants. Conclusion: We describe a neurodevelopmental disorder caused by (mainly) de novo variants in CTR9, likely affecting PAF1C function.

Original languageEnglish
Pages (from-to)1583-1591
Number of pages9
JournalGenetics in Medicine
Issue number7
StatePublished - Jul 2022


  • Autism spectrum disorder
  • CTR9
  • Intellectual disability
  • Neurodevelopmental disorder
  • PAF1C


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