Novel candidate genes and variants underlying autosomal recessive neurodevelopmental disorders with intellectual disability
Identification of Mendelian genes for neurodevelopmental disorders using exome sequencing to study autosomal recessive (AR) consanguineous pedigrees has been highly successful. To identify causal variants for syndromic and non-syndromic intellectual disability (ID), exome sequencing was performed using DNA samples from 22 consanguineous Pakistani families with ARID, of which 21 have additional phenotypes including microcephaly. To aid in variant identification, homozygosity mapping and linkage analysis were performed. DNA samples from affected family member(s) from every pedigree underwent exome sequencing. Identified rare damaging exome variants were tested for co-segregation with ID using Sanger sequencing. For seven ARID families, variants were identified in genes not previously associated with ID, including: EI24, FXR1 and TET3 for which knockout mouse models have brain defects; and CACNG7 and TRAPPC10 where cell studies suggest roles in important neural pathways. For two families, the novel ARID genes CARNMT1 and GARNL3 lie within previously reported ID microdeletion regions. We also observed homozygous variants in two ID candidate genes, GRAMD1B and TBRG1, for which each has been previously reported in a single family. An additional 14 families have homozygous variants in established ID genes, of which 11 variants are novel. All ARID genes have increased expression in specific structures of the developing and adult human brain and 91% of the genes are differentially expressed in utero or during early childhood. The identification of novel ARID candidate genes and variants adds to the knowledge base that is required to further understand human brain function and development.
We thank the families who participated in this study. We also thank the following who provided genotyping and sequencing services at the University of Washington Center for Mendelian Genomics (UW-CMG): Michael J. Bamshad1,2, Suzanne M. Leal3, and Deborah A. Nickerson1; Peter Anderson1, Marcus Annable1, Elizabeth E. Blue1, Kati J. Buckingham1, Imen Chakchouk3, Jennifer Chin1, Jessica X Chong1, Rodolfo Cornejo Jr.1, Colleen P. Davis1, Christopher Frazar1, Martha Horike-Pyne1, Gail P. Jarvik1, Eric Johanson1, Ashley N. Kang1, Tom Kolar1, Stephanie A. Krauter1, Colby T. Marvin1, Sean McGee1, Daniel J. McGoldrick1, Karynne Patterson1, Sam W. Phillips1, Jessica Pijoan1, Matthew A. Richardson1, Peggy D. Robertson1, Isabelle Schrauwen3, Krystal Slattery1, Kathryn M. Shively1, Joshua D. Smith1, Monica Tackett1, Alice E. Tattersall1, Marc Wegener1, Jeffrey M. Weiss1, Marsha M. Wheeler1, Qian Yi1, and Di Zhang3; Affiliations—1University of Washington; 2Seattle Children’s Hospital; 3Baylor College of Medicine. UW-CMG was funded by the National Human Genome Research Institute and the National Heart, Lung and Blood Institute grant HG006493 (to D. Nickerson, M. Bamshad and S. Leal). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This work was supported by funds from the Higher Education Commission, Islamabad, Pakistan (to W. Ahmad).
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