A de novo 1p34.2 microdeletion identifies the synaptic vesicle gene RIMS3 as a novel candidate for autism

Abstract

Background: A child with autism and mild microcephaly was found to have a de novo 3.3 Mb microdeletion on chromosome 1p34.2p34.3. The hypothesis is tested that this microdeletion contains one or more genes that underlie the autism phenotype in this child and in other children with autism spectrum disorders.

Methods: To search for submicroscopic chromosomal rearrangements in the child, array comparative genomic hybridisation (aCGH) was performed using a 19 K whole genome human bacterial artificial chromosome (BAC) array and the Illumina 610-Quad BeadChip microarray. Ingenuity pathway analysis (IPA) was used to construct functional biological networks to identify candidate autism genes. To identify putative functional variants in candidate genes, mutation screening was performed using polymerase chain reaction (PCR) based Sanger sequencing in 512 unrelated autism patients and 462 control subjects.

Results: A de novo 3.3 Mb deletion containing approximately 43 genes in chromosome 1p34.2p34.3 was identified and subsequently confirmed using fluorescence in situ hybridization (FISH). Literature review and bioinformatics analyses identified Regulating Synaptic Membrane Exocytosis 3 (RIMS3) as the most promising autism candidate gene. Mutation screening of this gene in autism patients identified five inherited coding variants, including one (p.E177A) that segregated with the autism phenotype in a sibship, was predicted to be deleterious, and was absent in 1161 controls.

Conclusions: This case report and mutation screening data suggest that RIMS3 is an autism causative or contributory gene. Functional studies of RIMS3 variants such as p.E177A should provide additional insight into the role of synaptic proteins in the pathophysiology of autism.

Figure 1

(A) The patient's head circumference (HC) was normal at birth, but decelerated after 7 months and subsequently followed a curve at −3 SD. Y axis shows HC size in both centimetres and inches. X axis indicates age. The top and bottom dashed curves represent HC at +2 SD (98%) and −2 SD (2%), respectively, in relation to the mean (50%) HC curve (solid). Serial HC measurements for the patient are represented as red dots. (B) The patient's facial appearance is normal at 1 year of age. (C) At 10 years the boy has subtle dysmorphism with a long narrow face and deep set or sunken eyes.

Figure 2

(A) Array comparative genome hybridisation (aCGH) using a bacterial artificial chromosome (BAC) microarray demonstrates a deletion in chromosome 1p34.2. The aCGH plot shows the log₂ ratio of the patient versus reference DNA on the vertical axis. Each individual BAC is represented as a single blue dot and the horizontal axis shows the position of each BAC along chromosome 1. The deletion of 1p34.2 is indicated by an arrow pointing to a vertical line of dots. Interrogation of the UCSC genome browser for the microdeletion region in this region identifies ∼47 RefSeq genes (shown below aCGH plot). Known copy number variants (CNVs) (orange blocks) and Indels (green blocks) are reported in the Database of Genomic Variants track. (B) Fluorescence in situ hybridisation (FISH) analysis confirms the deletion 1p34.2 aCGH results. The distal breakpoint boundary is indicated where RP11-67o15 (green arrows) shows two normal signals while RP11-120G12 (red arrow) shows a single signal in the interphase nucleus.

Figure 3

Mutation analysis of RIMS3 identifies two missense variants that segregate with autism and autism related phenotypes. (A) The pedigree for family AU0247 shows that the p.E177A missense variant is present in a patient with autism (AU0247-03), in a sibling with Not Quite Autism (NQA) (AU0247-04), and in the mother who presents with psychiatric symptoms. Chromatograms indicate the presence of the A/C substitution. The SIFT program predicted the p.E177A substitution to be deleterious. (B) The pedigree for family AU0125 shows that the p.M260V missense variant is present in two siblings with autism (AU0125-03 and AU0125-04) as well as in the father who presents with psychiatric symptoms, including obsessive–compulsive disorder (OCD). Chromatograms indicate the presence of the A/G substitution. The variant is not predicted to affect protein function.