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Case Reports
. 2020 Sep;8(9):e1364.
doi: 10.1002/mgg3.1364. Epub 2020 Jun 26.

Diagnostic utility of integrated analysis of exome and transcriptome: Successful diagnosis of Au-Kline syndrome in a patient with submucous cleft palate, scaphocephaly, and intellectual disabilities

Mamiko Yamada  1 , Yuichi Shiraishi  2 , Tomoko Uehara  1 , Hisato Suzuki  1 , Toshiki Takenouchi  3 , Chihiro Abe-Hatano  4 , Kenji Kurosawa  4 , Kenjiro Kosaki  1
Affiliations
Case Reports

Diagnostic utility of integrated analysis of exome and transcriptome: Successful diagnosis of Au-Kline syndrome in a patient with submucous cleft palate, scaphocephaly, and intellectual disabilities

Mamiko Yamada et al. Mol Genet Genomic Med. 2020 Sep.

Abstract

Background: A weakness of exome analysis lies in inability to characterize aberrant splicing other than those involving consensus donor-acceptor sequence. To overcome this limitation, we developed a novel analytic method SAVNet that combines transcriptome and exome analysis which enabled the successful detection of carriers of splicing variants in the disease-causing genes of autosomal recessive disorders within a normal cohort. However, the clinical utility of the SAVNet analysis in delineating splicing defects in patients without a diagnosis has yet to be documented.

Method: We performed SAVNet analysis using the integrated analysis of exome and transcriptome analysis from the peripheral blood of the patient. The patient is an undiagnosed Japanese female patient with submucous cleft palate, scaphocephaly and intellectual disability with no words at 8 years of age. Dysmorphic features included a long face, a short palpebral fissure, thick lips with an open month, premaxillary hypoplasia, a depressed nasal bridge, and satyr ears.

Result: A SAVNet analysis showed that a heterozygous intronic variant located at the -10 position of exon 5 of the HNRNPK gene on chromosome 9 created a new splice acceptor sequence "ag" and led to the incorporation of 9 intronic nucleotides into the coding sequence. The mutant protein would have three extra amino acid residues, Leu-Leu-Gln, inserted within the critical KH domain. The patient was diagnosed as having recently delineated Au-Kline syndrome, which is characterized by cleft palate, craniosynostosis, and intellectual disability.

Conclusion: The successful molecular diagnosis of the presently reported patient illustrates the diagnostic utility of the SAVNet analysis as an innovative way of implementing an integrated exome-transcriptome analysis in clinical settings.

Keywords: HNRNPK; Au; Kline syndrome; RNA-seq; integrated analysis; splicing.

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Conflict of interest statement

The authors have no conflicts of interest to disclose.

Figures

Figure 1
Figure 1
Facial features of the patient at the age of 8 years. Characteristic features included a long face, a short and downslanting palpebral fissures, thick lips with an open mouth, premaxillary hypoplasia, a depressed nasal bridge, and satyr ears
Figure 2
Figure 2
Abnormal splicing of HNRNPK detected by SAVNet analysis. A rare single nucleotide substitution chr9(GRCh37):g.86591976A>C affects splicing at the donor end of the fourth intron. The top portion of the figure depicts results of the transcriptome analysis of the patient as the sashimi plot. Some of the read derived from the patient had an extension of the exon toward the 5’ direction in comparison with the normal pattern (blue boxes). The middle portion of the figure shows the magnified view of the top portion. The bottom portion of the figure depicts effect of abnormal splicing on deduced amino acid sequence. The chr9(GRCh37):g.86591976A>C corresponds to a substitution of “t” to “g” at the −10 position of exon 5 of HNRNPK. This base change created a new splice acceptor site “ag” and led to incorporation of 9 intronic nucleotides into the coding sequence. The mutant protein will have three extra amino acid residues Leu‐Leu‐Gln inserted
See this image and copyright information in PMC

References

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