Identification and functional modelling of plausibly causative cis -regulatory variants in a highly-selected cohort with X-linked intellectual disability

Change log

Identifying causative variants in cis-regulatory elements (CRE) in neurodevelopmental disorders has proven challenging. We have used in vivo functional analyses to categorize rigorously filtered CRE variants in a clinical cohort that is plausibly enriched for causative CRE mutations: 48 unrelated males with a family history consistent with X-linked intellectual disability (XLID) in whom no detectable cause could be identified in the coding regions of the X chromosome (chrX). Targeted sequencing of all chrX CRE identified six rare variants in five affected individuals that altered conserved bases in CRE targeting known XLID genes and segregated appropriately in families. Two of these variants, FMR1CRE and TENM1CRE, showed consistent site- and stage-specific differences of enhancer function in the developing zebrafish brain using dual-color fluorescent reporter assay. Mouse models were created for both variants. In male mice Fmr1CRE induced alterations in neurodevelopmental Fmr1 expression, olfactory behavior and neurophysiological indicators of FMRP function. The absence of another likely causative variant on whole genome sequencing further supported FMR1CRE as the likely basis of the XLID in this family. Tenm1CRE mice showed no phenotypic anomalies. Following the release of gnomAD 2.1, reanalysis showed that TENM1CRE exceeded the maximum plausible population frequency of a XLID causative allele. Assigning causative status to any ultra-rare CRE variant remains problematic and requires disease-relevant in vivo functional data from multiple sources. The sequential and bespoke nature of such analyses renders them time-consuming and challenging to scale for routine clinical use.


Funder: BBSRC studentship

Research Article, Research and analysis methods, Biology and life sciences, Medicine and health sciences
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Public Library of Science
Medical Research Foundation (MRC University Unit Grant to University of Edinburgh)
Medical Research Council (GB) (MRC University Unit Grant to University of Edinburgh)
Newlife – The Charity for Disabled Children (GB) (14-15/07)
European Union FP7 (HEALTH- F4-2009-223262)
National Institute for Health Research (GB) (NIHR Cambridge Biomedical Research Centre grant)
French Government (ANR–10–LABX–54 MEMOLIFE and ANR–10–IDEX–0001–02 PSL)
Simons Foundation (US) (Simons Initiative for the Developing Brain)
National Institute for Health Research (NIHR Cambridge Biomedical Research Centre grant)
National Institute of Health Research Bioresource for Rare Diseases (RG65966)