Missense-depleted regions in population exomes implicate ras superfamily nucleotide-binding protein alteration in patients with brain malformation.

Yvonne Hendriks,Kevin Dumas,Pui-Yan Kwok,Jessica Litwin,Marjan M Weiss,Henry Gong,Joanna J Phillips,Kyra E Stuurman,Quinten Waisfisz,Stanley F Nelson,Xiaoyan Ge,Joseph T C Shieh,Wayne W Grody,Hane Lee

doi:10.1038/npjgenmed.2016.36

Abstract

Genomic sequence interpretation can miss clinically relevant missense variants for several reasons. Rare missense variants are numerous in the exome and difficult to prioritise. Affected genes may also not have existing disease association. To improve variant prioritisation, we leverage population exome data to identify intragenic missense-depleted regions (MDRs) genome-wide that may be important in disease. We then use missense depletion analyses to help prioritise undiagnosed disease exome variants. We demonstrate application of this strategy to identify a novel gene association for human brain malformation. We identified de novo missense variants that affect the GDP/GTP-binding site of ARF1 in three unrelated patients. Corresponding functional analysis suggests ARF1 GDP/GTP-activation is affected by the specific missense mutations associated with heterotopia. These findings expand the genetic pathway underpinning neurologic disease that classically includes FLNA. ARF1 along with ARFGEF2 add further evidence implicating ARF/GEFs in the brain. Using functional ontology, top MDR-containing genes were highly enriched for nucleotide-binding function, suggesting these may be candidates for human disease. Routine consideration of MDR in the interpretation of exome data for rare diseases may help identify strong genetic factors for many severe conditions, infertility/reduction in reproductive capability, and embryonic conditions contributing to preterm loss.

Highlights

Genomic sequencing reveals many rare or private heterozygous missense variants per person
When we initially examine the variant pattern from population exome data looking for gene level missense depletion, the overall missense depletion is modest in disease genes, the greatest difference is seen in genes for dominant or X-linked conditions, which are reported to account for approximately 50% of all diagnoses made for trio clinical exomes.[10,11,12]
With ARF1 protein, we demonstrate that missense variation near the nucleotide-binding site of ARF1 alters activation and places RESULTS

Summary

INTRODUCTION

Genomic sequencing reveals many rare or private heterozygous missense variants per person. The affected residue p.K127 is known to be important in functional studies of ARF1 in other systems.[21,22] A third patient had a de novo missense variant in ARF1 c.296G4A (p.R99H) and had brain malformation with delayed myelination in childhood and significant cerebral underdevelopment 12 years later, and p.R99 appears to contact two of the GDP-binding residues of ARF1 by LPC/CSU analysis (Figure 3 and Supplementary Table 7). The third individual had limited information available but had seizures and periventricular heterotopia These results further emphasise the importance of variant prioritisation based on the location of intragenic missense variants, nucleotide-binding proteins and missense depletion regions. ARF1 is likely in a molecular pathway with known genes for periventricular heterotopia including FLNA and ARFGEF2, the gene encoding the ARF-activator protein BIG223 These results indicate that exome variants may be prioritised using missense depletion methods from population exome data independent of knowledge of a gene or gene region's function

DISCUSSION

MATERIALS AND METHODS

Findings

Code availability