Segmental Maternal UPD of Chromosome 7q in a Patient With Pendred and Silver Russell Syndromes-Like Features

Abstract

Pendred syndrome (PS) is an autosomal recessive disorder due to mutations in the SLC26A4 gene (chr7q22. 3) and characterized by sensorineural hearing loss and variable thyroid phenotype. Silver-Russell syndrome (SRS) is a heterogeneous imprinting disorder including severe intrauterine and postnatal growth retardation, and dysmorphic features. Maternal uniparental disomy of either the whole chromosome 7 (upd(7)mat) or 7q (upd(7q)mat) is one of the multiple mechanisms impacting the expression of imprinted genes in SRS, and is associated with milder clinical features. Here, we report genetic and clinical characterization of a female child with PS, postnatal growth retardation, and minor dysmorphic features. A gross homozygous deletion of SLC26A4 exons 17-20 was suspected by Sanger sequencing and then confirmed by array-CGH. Moreover, an insertion of about 1 kb of the CCDC126 gene (7p15.3), which does not appear to be clinically relevant, was detected. The possible occurrence of a balanced rearrangement between 7p and 7q was excluded. The absence of the deletion in the father led to the investigation of upd, and microsatellite segregation analysis revealed a segmental 7q (upd(7q)mat), leading to SLC26A4 homozygosity and responsible for both PS and SRS-like traits. The proband matched 3 out of 6 major SRS criteria. In conclusion, this is the first report of uniparental isodisomy encompassing almost the whole long arm of chromosome 7 resulting in PS and SRS-like features. Whereas, the inner ear phenotype of PS is typical, the clinical features suggestive of SRS might have been overlooked.

Keywords: SLC26A4; pendred syndrome; post-natal growth retardation; silver-russell syndrome; uniparental disomy.

Figure 1

Clinical and molecular characterization of the case. (A) Frontal and lateral view of the proband at the age of 36 months. Note the mild frontal bossing, low-set posteriorly rotated ears, and thin lips. Earing aids are in place. The patient also displays brachydactyly of both hands and feet and clinodactily of V finger of hands. Other clinical findings are listed in the side table, where 3 out of 6 NH-CSS for SRS are in bold characters. (B) The LR-PCR amplicons of the patient (P) and both her father (F) and mother (M) were resolved on a 0.8% agarose gel. The patient (P) displayed a unique shorter band of about 2.5 kb in size, the father (F) showed a unique band of over 10 kb in size, corresponding to the expected 14.7 kb wild type band, whereas her mother (M) showed two bands corresponding to the wild type and the deleted alleles. MW, molecular weight. (C) The proximal and distal breakpoints of the SLC26A4 intragenic deletion were mapped within SLC26A4 IVS16 and the IVS20, respectively. The deletion is about 13 kb long. Sequence alignments of the junction fragments revealed an insertion of a part of CCDC126 IVS3. The rejoining between SLC26A4 IVS20 and CCDC126 IVS3 distal bkp occurred through a de novo 3 bp GCC insertion. (D) Sequencing of the RT-PCR amplicons, extending from exons 13–14 to 3′UTR of SLC26A4, confirmed the homozygous deletion of exons 17–20 in the child (P). The father (F) showed only the long transcript corresponding to the wild type pendrin, whereas the mother (M) displayed a short transcript and a long one, consistent with a heterozygous state of the deletion. MW, molecular weight.

Figure 2

Cytogenetic and molecular characterization of upd(7)mat (A) Q-banding ruled out any apparently balanced structural rearrangement in the chromosome 7 homologous of both the patient (a) and her mother (b). (c) Identification in the patient of a 6 kb homozygous deletion within the SLC26A4 gene at 7q22.3 (minimum interval chr7:107344703_107350605, GRCh37/hg19) using Agilent CGH 400K array. The mother resulted heterozygous for the same deletion. (B) Family pedigree: filled symbol indicates the homozygous-affected proband and symbol with dot denotes carrier mother. Parents-to-proband segregation of alleles at 21 microsatellites spanning chromosome 7 is shown. STR markers mapping within the disomic region are highlighted in red, the markers showing the lack of paternal contribution are bolded. (C) MS-MLPA profile of the imprinted loci at chromosomes 6, 7, and 14 in the proband. Copy number quantification (top panel) and methylation ratio (bottom panel) for GRB10:alt-TSS-DMR and MEST:alt-TSS-DMR are shown. Each black dot displays the final probe ratio for each locus analyzed, and refers to the interval of values obtained by reference samples (light blue rectangles). The red and blue lines indicate the arbitrary borders for loss and gain, respectively. By default, the borders are placed ±0.3 from the mean probe value of a probe over the reference samples. No deviation from reference samples is observed for CNVs, indicating a biallelic contribution (top panel). The MS profile shows a gain of methylation (methylation ratio = 1) for the paternally imprinted MEST:alt-TSS-DMR in the proband, as shown by blue dots, with respect to reference samples (methylation ratio = 0.5). On the contrary, a proper methylation is observed at the GRB10:alt-TSS-DMR, as shown by black dots (bottom panel). Standard deviations were set up according to the Coffalyzer DB software v131211. (D) SNP array profile of patient chromosome 7. Top plot shows B allele frequency revealing an 83.5 Mb isodisomic region (7q11.23-qter) including PEG10:TSS-DMR, MEST:alt-TSS-DMR, and HTR5A:TSS-DMR imprinted loci; bottom plot shows Log R ratio, which reveals a proper biallelic contribution.