This study was approved by our
This study was approved by our institutional ethics committee, and informed consent was obtained from each participant or legal guardian. We performed whole-genome SNP genotyping in the one unaffected and two affected siblings by using the Illumina Human 610 Genotyping BeadChip panel, which interrogates 620,901 SNPs. Given that transmission of the phenotype in this family was consistent with autosomal-recessive inheritance and that the parents were consanguineous, we used PLINK to identify regions that contained >30 consecutive SNPs, extended over >1 Mb, and were homozygous in both affected individuals but not in the unaffected sibling. We then performed whole-exome sequencing in affected individual A.II-3. Blood genomic DNA was captured with the Agilent SureSelect Human All Exon Capture V4 Kit and sequenced (two paired-end 100 bp reads and four exomes per lane) with an Illumina HiSeq 2000 at the McGill University Genome Quebec Innovation Center. Sequence processing, alignment (with a Burrows-Wheeler algorithm), and variant calling were performed according to the Broad Institute Genome Analysis Toolkit (GATK v.4) Best Practices, and variants were annotated with ANNOVAR. The average exome coverage of the target bases was 119×, and 95% of the target bases were covered by at least ten reads. Only the variants whose positions were covered ≥8× and supported by at least three variant reads constituting at least 20% of the total reads for each called position were retained. To identify potentially pathogenic variants, we selected variants affecting coding and splice sites that were present at minor allele frequencies (MAFs) ≤ 0.005 in public databases (e.g., 1000 Genomes and NHLBI Exome Sequencing Project [ESP] Exome Variant Server) and ≤1% in in-house control datasets. We found no rare homozygous or potentially compound-heterozygous variants in 7915 associated with ID. We then searched the whole-exome dataset for genes harboring homozygous variants in the previously identified homozygous regions (≥1Mb) shared by the two affected sisters but not by their unaffected sibling. Segregation of these variants within the family was confirmed by Sanger sequencing. Variants that were found to be homozygous in the parents were excluded. The five homozygous variants that remained after our segregation analysis were screened in 95 ethnically matched control individuals. Three variants were excluded because they were observed at high frequencies, which are incompatible with a rare recessive disease. The variant c.153C>A (p.Cys51X) in MIB2 (OMIM: 611141; GenBank: NM_001170688.1) was identified in 3.2% (3/95) of control individuals, c.2103C>A (p.Asp701Glu) in MMEL1 (GenBank: NM_033467.3) was found in 3.2% (3/95), and c.2135G>A (p.Cys712Tyr) in ANLN (OMIM: 616027; GenBank: NM_018685.4) was found in 2.1% (2/95). The remaining candidate variants, c.629C>T (p.Ala210Val) in SLC45A1 (OMIM: 605763; GenBank: NM_001080397.1) and c.1225C>T (p.Arg409Trp) in TNFRSF8 (OMIM: 153243; GenBank: NM_001243.4), were both absent in the 95 ethnically matched control individuals. TNFRSF8 is a member of the tumor necrosis factor receptor superfamily and is a surface antigen used as a clinical marker for Hodgkin lymphoma and related hematologic malignancies. It has no known role in neurodevelopment and is not highly expressed in the brain (Human Protein Atlas). The c.1225C>T (p. Arg409Trp) variant is rare (MAF = 0.00001660 in the Exome Aggregation Consortium [ExAC] Browser) and predicted to be benign by PolyPhen-2 (score = 0.008) and SIFT (score = 0.39). SLC45A1 encodes a glucose transporter that is highly prevalent in the brain. The c.629C>T (p.Ala210Val) variant is rare (MAF = 0.0001497 in the ExAC Browser) and predicted to be damaging by PolyPhen-2 (score = 0.999) and SIFT (score = 0.000). In parallel, we identified two ID-affected brothers from the United Arab Emirates, and their parents are also first-degree cousins (Figure 1A). Individual B.II-3 is currently 8 years old and was born after an unremarkable pregnancy and delivery. His birth weight was 2.8 kg (10th percentile), but length and head circumference were not recorded. His development was globally delayed. He walked at 2.5 years and is now able to run and go up and down stairs. He is nonverbal and only produces sounds and jargon. He does not understand simple instructions. He has good eye contact but does not point to needs, share interests, or seek social interaction. He has no pretend play. He spins and flaps his hands. He has had several assessments for a diagnosis of autism, but formal assessment gave conflicting results. He is able to eat with his fingers but does not use cutlery. He needs assistance in most activities of daily living and is not toilet trained. He had one febrile seizure at the age of 7 months and then one afebrile secondarily generalized seizure at the age of 9 months, after which he was started on levetiracetam. The parents discontinued the anticonvulsant when the child was 12 months old, and he has not had any seizure recurrence. EEG revealed enhanced spike-and-slow-wave activity in the left occipital region during sleep, as well as slowing of the background in the left occipital region in the form of polymorphic delta waves. Photosensitivity and electrical status epilepticus during sleep were absent. This individual has a single left kidney. Hyperparathyroidism was diagnosed at the age of 6 years, and hypercalcemia and hypophosphatemia were noted in the context of routine blood work, although the individual was asymptomatic. Head circumference at the age of 18 months was at the 10th percentile. On physical examination at 8 years, his height was 118 cm (3rd percentile), and his weight was 19 kg (<3rd percentile). He has a triangular face, downslanting eyes, arched eyebrows, a smooth philtrum, and thin lips. His neurological examination was unremarkable. Investigations that included brain MRI, chromosomal microarray, fragile X testing, transferrin isoelectric focusing, and echocardiography were normal.