X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

Abstract

X-linked intellectual disability (XLID) is a clinically and genetically heterogeneous disorder. During the past two decades in excess of 100 X-chromosome ID genes have been identified. Yet, a large number of families mapping to the X-chromosome remained unresolved suggesting that more XLID genes or loci are yet to be identified. Here, we have investigated 405 unresolved families with XLID. We employed massively parallel sequencing of all X-chromosome exons in the index males. The majority of these males were previously tested negative for copy number variations and for mutations in a subset of known XLID genes by Sanger sequencing. In total, 745 X-chromosomal genes were screened. After stringent filtering, a total of 1297 non-recurrent exonic variants remained for prioritization. Co-segregation analysis of potential clinically relevant changes revealed that 80 families (20%) carried pathogenic variants in established XLID genes. In 19 families, we detected likely causative protein truncating and missense variants in 7 novel and validated XLID genes (CLCN4, CNKSR2, FRMPD4, KLHL15, LAS1L, RLIM and USP27X) and potentially deleterious variants in 2 novel candidate XLID genes (CDK16 and TAF1). We show that the CLCN4 and CNKSR2 variants impair protein functions as indicated by electrophysiological studies and altered differentiation of cultured primary neurons from Clcn4−/− mice or after mRNA knock-down. The newly identified and candidate XLID proteins belong to pathways and networks with established roles in cognitive function and intellectual disability in particular. We suggest that systematic sequencing of all X-chromosomal genes in a cohort of patients with genetic evidence for X-chromosome locus involvement may resolve up to 58% of Fragile X-negative cases.

Intragenic FMR1 disease-causing variants: a significant mutational mechanism leading to Fragile-X syndrome

“…4 CGG-repeat expansion in the FMR1 promoter is the most frequent cause of FXS, but deletions of the entire FMR1 gene [10][11][12] or of the 5′UTR have also been reported in FXS. 9 Rare intragenic non-synonymous variations have also been identified within the FMR1 locus [16][17][18][19][20]22,23,35,41,42 but after reanalysis in the light of new public sequencing data, prediction tools and functional evidence, we showed that only six could be reclassified as convincing.…”

“…We have also compiled the rare non-synonymous variants identified in FMR1 during large-scale studies (large panel, X-exome or wholeexome sequencing) performed on ID patients by other teams: only missense variants but no truncating variants were identified in the 3180 individuals tested. [33][34][35][36][37][38][39][40][41][42] We reanalyzed all these variants in FMR1 in the light of new public sequencing data (Exome Variant Server and the ExAC project, supposed to be free or at least not enriched in severe developmental disorders), prediction tools and functional evidence. Altogether, six previously reported variants could also be reclassified as disease-causing (pathogenic-class 5 or likely pathogenic-class 4 variants, summarized in Table 3 and in Figure 4).…”

Hypomorphic Pathogenic Variants in TAF13 Are Associated with Autosomal-Recessive Intellectual Disability and Microcephaly

“…The effect was particularly marked with the c.119T>A (p.Met40Lys) variant. In addition to these clinical, genetic, modeling, and biochemical results, the fact that mutations in other components of the TFIID complex (TAF1, TAF2, TAF6, and TBP) lead to a neurological phenotype [8][9][10][11][12][13][14][15] strongly supports our hypothesis that bi-allelic pathogenic alterations in the histone fold domain of TAF13 lead to mild ID and microcephaly. TAF13 is a constituent of at least two protein complexes: the TFIID complex and the small nuclear RNA genespecific TAF complex (snTAFc), which play a critical role in the regulation of gene transcription in eukaryotic cells.…”

“…Intriguingly, in other subunits of TFIID, different variants lead to different phenotypes. Variants in TAF1 are associated with ID and microcephaly 13,14 whereas the reduction in TAF1 expression is associated with XDP 10 (Table S1). Also, in TBP, the expansion of the polyglutamine (polyQ) tract causes SCA17 probably in a gain-of-function mode, whereas heterozygous deletion of TBP is probably responsible for ID and microcephaly 9,29 (Table S1).…”

The Use of Next-Generation Sequencing for Research and Diagnostics for Intellectual Disability

“…There are still many likely X-linked cases in which there is no molecular diagnosis. Hu et al (2015) performed a study on 405 families, which had clear familial evidence of XLID. These families were termed unresolved because despite microarray-based copy number variation (CNV) analysis and Sanger sequencing of a subset of XLID genes there was no definitive cause of ID.…”