In silico prioritization and further functional characterization of SPINK1 intronic variants

Zou, Wen-Bin, Wu, Hao, Boulling, Arnaud, Cooper, David Neil ORCID: https://orcid.org/0000-0002-8943-8484, Li, Zhao-Shen, Liao, Zhuan, Chen, Jian-Min and Férec, Claude 2017. In silico prioritization and further functional characterization of SPINK1 intronic variants. Human Genomics 11 (7) 10.1186/s40246-017-0103-9

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Abstract

Background SPINK1 (serine protease inhibitor, kazal-type, 1), which encodes human pancreatic secretory trypsin inhibitor, is one of the most extensively studied genes underlying chronic pancreatitis. Recently, based upon data from qualitative reverse transcription-PCR (RT-PCR) analyses of transfected HEK293T cells, we concluded that 24 studied SPINK1 intronic variants were not of pathological significance, the sole exceptions being two canonical splice site variants (i.e., c.87 + 1G > A and c.194 + 2T > C). Herein, we employed the splicing prediction tools included within the Alamut software suite to prioritize the ‘non-pathological’ SPINK1 intronic variants for further quantitative RT-PCR analysis. Results Although our results demonstrated the utility of in silico prediction in classifying and prioritizing intronic variants, we made two observations worth noting. First, we established that most of the prediction tools employed ignored the general rule that GC is a weaker donor splice site than the canonical GT site. This finding is potentially important because for a given disease gene, a GC variant donor splice site may be associated with a milder clinical manifestation. Second, the non-pathological c.194 + 13T > G variant was consistently predicted by different programs to generate a new and viable donor splice site, the prediction scores being comparable to those for the physiological c.194 + 2T donor splice site and even higher than those for the physiological c.87 + 1G donor splice site. We do however provide convincing in vitro evidence that the predicted donor splice site was not entirely spurious. Conclusions Our findings, taken together, serve to emphasize the importance of functional analysis in helping to establish or refute the pathogenicity of specific intronic variants.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Medicine
Subjects:	R Medicine > R Medicine (General)
Uncontrolled Keywords:	Aberrant mRNA transcripts – Chronic pancreatitis – In silico – Intronic variants – Non-canonical splice sites – Quantitative RT-PCR analysis – SPINK1 – Splicing phenotype prediction
Publisher:	Henry Stuart Publications
ISSN:	1479-7364
Date of First Compliant Deposit:	16 May 2017
Date of Acceptance:	20 April 2017
Last Modified:	07 Nov 2023 09:07
URI:	https://orca.cardiff.ac.uk/id/eprint/100596

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