Duplication of C7orf58, WNT16 and FAM3C in an obese female with a t(7;22)(q32.1;q11.2) chromosomal translocation and clinical features resembling Coffin-Siris Syndrome

Abstract

We characterized the t(7;22)(q32;q11.2) chromosomal translocation in an obese female with coarse features, short stature, developmental delay and a hypoplastic fifth digit. While these clinical features suggest Coffin-Siris Syndrome (CSS), we excluded a CSS diagnosis by exome sequencing based on the absence of deleterious mutations in six chromatin-remodeling genes recently shown to cause CSS. Thus, molecular characterization of her translocation could delineate genes that underlie other syndromes resembling CSS. Comparative genomic hybridization microarrays revealed on chromosome 7 the duplication of a 434,682 bp region that included the tail end of an uncharacterized gene termed C7orf58 (also called CPED1) and spanned the entire WNT16 and FAM3C genes. Because the translocation breakpoint on chromosome 22 did not disrupt any apparent gene, her disorder was deemed to result from the rearrangement on chromosome 7. Mapping of yeast and bacterial artificial chromosome clones by fluorescent in situ hybridization on chromosome spreads from this patient showed that the duplicated region and all three genes within it were located on both derivative chromosomes 7 and 22. Furthermore, DNA sequencing of exons and splice junctional regions from C7orf58, WNT16 and FAM3C revealed the presence of potential splice site and promoter mutations, thereby augmenting the detrimental effect of the duplicated genes. Hence, dysregulation and/or disruptions of C7orf58, WNT16 and FAM3C underlie the phenotype of this patient, serve as candidate genes for other individuals with similar clinical features and could provide insights into the physiological role of the novel gene C7orf58.

Figure 1. CNVs on chromosomes 1, 4, 15 and 16 of the index patient revealed by Agilent 244K human genome CGH microarray hybridization.

The profiles shown represent the averaged combined hybridization data of patient vs. reference DNA. Regions of gain and losses are boxed and depicted as positive or negative log₂ ratios relative to the midline that denotes no gain/no loss of DNA sequences.

Figure 2. Array CGH array of the index patient showing duplication and amplification of DNA sequences on chromosomes 7 and 22.

(A) Chromosome 7 and 22 plots displaying gains of DNA sequences, shown in boxes, in the 7q31.3 and 7q22 regions. (B, C) Detailed plots of oligonucleotide probes from the microarray along each region of interest denoting the genes and their chromosomal coordinates (hg18) in the duplicated and amplified regions of chromosomes 7 and 22, respectively.

Figure 3. Representative fluorescent in situ hybridization (FISH) patterns of DNA probes onto chromosomes 7, 22 der(7) and der(22) from this patient’s chromosome spreads.

(A) Schematic drawing of normal chromosomes 7 and 22 and derivative chromosomes der(7) and der(22), showing the translocated chromosomal regions. The three panels below depict each the typical hybridization of a probe located (B) on chromosomes 7, der(7), (C) on chromosomes 7, der(7), der(22) and (D) chromosomes 7 and der(22).

Figure 4. FISH maps of YAC and BAC DNA clones from chromosome 7q31.1 in and around the duplicated region.

The hg19 genomic coordinates of each marker and gene are indicated next to its designated name. The centromeric (CEN) and telomeric (TEL) directions are specified for orientation on the chromosome. Clones are denoted by their clone names, plate coordinates or/and Genbank designations. Each clone or restriction fragment is also denoted by its hybridization onto the patient’s chromosomes 7, der(7) and/or der(22). (A) FISH map of a 12.9 Mb region of chromosome 7 extending from the CFTR to the CPA1 genes. The denoted YAC probes represent three distinct areas of hybridization relative to the chromosome 7 translocation breakpoint, namely distal (7, der22), at or around the breakpoint (7, der7, der22) and proximal to the breakpoint (7, der7). (B) FISH map of BAC clones at and proximal to the 434,682 bp duplicated region, spanning the tail end of C7orf58 and the entire WNT16 and FAM3C genes. Note that all BAC clones within the duplicated region map to 7,d7,d22. (C) Bam HI restriction map, except for two designated Hind III (H) sites, of BAC 146J04 showing the FISH mapping of Bam HI and Hind III restriction fragments, indicating hybridization to 7,der(7) and der(22). The sizes in bp of each restriction fragment are shown and the exons in each gene displayed with solid boxes. The initiation (ATG) and termination (TGA, TAA) codons denote the gene boundaries except for C7orf58, which is only spanned by its last exon and part of the adjacent intron.