Acquired uniparental disomy of chromosome 7 in a patient with MIRAGE syndrome that veiled a pathogenic SAMD9 variant

Abstract

Gain-of-function variants in SAMD9, which resides on chromosome 7, cause MIRAGE syndrome that is associated with congenital adrenal insufficiency and gonadal dysgenesis. We previously reported a Japanese patient with MIRAGE syndrome carrying a de novo heterozygous SAMD9 variant (p.Ala1479Ser). In this study, we confirmed the pathogenicity of Ala1479Ser-SAMD9 in vitro. Genetic study results revealed an atypically low variant allele frequency (26%) and we suspected of genomic rearrangement(s) involving chromosome 7. Single nucleotide polymorphism (SNP) array and short tandem repeat analysis showed presence of mosaic maternal isodisomic uniparental disomy 7 (UPD7). Deep sequencing using DNA samples obtained at 0, 6, 10, and 25 mo of age revealed that the percentage of cells with UPD7 increased constantly from 6% to 82% over 25 mo, and this increase coincided with a decrease in the percentage of cells with p.Ala1479Ser from 94% to nearly undetectable levels. We further screened for low-allele-frequency and rare SAMD9 variants in eight patients with Silver-Russel syndrome and maternal UPD7; however, none of the patients harbored such a variant. In conclusion, our case demonstrates that genetic findings can vary considerably in patients with MIRAGE syndrome and that a comprehensive diagnostic approach, including SNP array and deep sequencing, is important in such cases.

Keywords: MIRAGE syndrome; Silver-Russell syndrome; uniparental disomy.

Fig. 1.

Functional analysis of Ala1479Ser-SAMD9. Growth of HEK293 cells that overexpressed SAMD9 [wildtype (WT) or Ala1479Ser] was monitored with a time-lapse microscope for 144 h. Note that expression of Ala1479Ser-SAMD9 caused profound growth restriction, which is a characteristic of MIRAGE syndrome-associated variants. Values represent the mean ± SEM (n = 3).

Fig. 2.

Copy number variation analysis and loss of heterozygosity (LOH) analysis. (A) Single nucleotide polymorphism (SNP) array analysis using the DNA obtained at the age of 10 mo showed copy-neutral LOH on chromosome 7q (i.e., isodisomic UPD7q). The shaded area represents LOH. A vertical bar denotes 7q21.2, where SAMD9 resides. (B) Evaluation of the short tandem repeat marker D7S515 indicated the presence of mosaic maternal isodisomic UPD7. The signal derived from the paternal allele (highlighted as “F”) was detectable yet relatively low as compared with the signal derived from the maternal allele (highlighted as “M”).

Fig. 3.

Chronological evaluation of the three cell types in the patient’s hematopoietic system. (A) A line graph showing variant allele frequencies (VAFs) of Ala1479Ser (solid circles) and Arg824Ter (open circles) analyzed by deep sequencing. Shaded areas represent 95% confidence intervals. (B) Chronological changes of short tandem repeat analysis at locus D7S515. The signal derived from the paternal allele (highlighted as “F”) showed constant decrease over time compared to the signal derived from the maternal allele (highlighted as “M”). (C) Fraction of the three types of cells estimated from VAFs of Ala1479Ser and Arg824Ter. The data corresponding to cells with Ala1479Ser only, those with Ala1479Ser and Arg824Ter, and those with maternal UPD7q are shown in red, grey and blue, respectively.