Mutations in the BAF-complex subunit DPF2 associated with Coffin-Siris syndrome

Variants affecting the function of different subunits of the BAF chromatin remodelling complex lead to various neurodevelopmental syndromes including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental delay disorders. Here we report 8 heterozygous de novo variants, 1 frameshift, 2 splice site and 5 missense, in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2). Affected individuals share common clinical features described in individuals with Coffin-Siris syndrome including coarse facial features, global developmental delay, intellectual disability, speech impairment and hypoplasia of finger and toenails. All variants occur within the highly conserved PHD1 and PHD2 motifs. Moreover, missense variants are situated close to zinc binding sites and are predicted to disrupt these sites. Recombinant protein and histone peptide pull-down assays revealed that a subset of the identified missense variants abolished or impaired DPF2 binding to unmodified and modified H3 histone tails. These results suggest an impairment of PHD fingers structural integrity and cohesion and likely an aberrant recognition of histone modifications. Furthermore, in HEK293 and COS7 cell lines the overexpression of these variants was associated with nuclear aggregate formation and recruitment of both wild-type DPF2 and BRG1 to these aggregates. Expression analysis of truncating variants found in individuals, indicated that the aberrant transcripts escape nonsense-mediated decay. Taken together, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant negative mechanism of pathogenicity

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

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