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Identification of novel deep intronic PAH gene variants in patients with phenylketonuria
  • +8
  • Xiaohua Jin,
  • Yousheng Yan,
  • Chuan Zhang,
  • Ya Tai,
  • Lisha An,
  • Xinyou Yu,
  • Linlin Zhang,
  • Xiaofang Cao,
  • Shengju Hao,
  • Chenghong Yin,
  • Xu MA
Xiaohua Jin
National Research Institute for Family Planning
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Yousheng Yan
Capital Medical University Beijing Obstetrics and Gynecology Hospital
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Chuan Zhang
Gansu Provincial Maternity and Child-Care Hospital
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Ya Tai
Peking University International Hospital
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Lisha An
National Research Institute for Family Planning
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Xinyou Yu
General Hospital of Ningxia Medical University
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Linlin Zhang
The Third Affiliated Hospital of Zhengzhou University
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Xiaofang Cao
National Research Institute for Family Planning Center for Genetics
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Shengju Hao
Gansu Provincial Maternity and Child-Care Hospital
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Chenghong Yin
Capital Medical University Beijing Obstetrics and Gynecology Hospital
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Xu MA
National Research Institute for Family Planning, Peking Union Medical College
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Abstract

Phenylketonuria (PKU) is caused by phenylalanine hydroxylase (PAH) gene variants. Previously, 94.21% of variants were identified using Sanger sequencing and multiplex ligation-dependent probe amplification. To investigate the remaining variants, whole-genome sequencing (WGS) was performed in four patients with PKU with unknown genotype to identify deep intronic or structural variants. Three novel heterozygous variants (c.706+368T>C; c.1065+241C>A; and c.1199+502A>T) were identified in a deep PAH gene intron. The c.1199+502A>T variant was detected in 60% (6/10) PKU patients. In silico prediction showed that the three deep variants may impact splice site selection and result in inclusion of a pseudo-exon. The c.1199+502A>T PAH minigene and reverse transcription PCR of blood RNA in a patient with PKU and compound heterozygous variants (c.1199+502A>T/ c.1199G>A) confirmed that the c.1199+502A>T variant creates a novel branch point and leads to the inclusion of a 25 bp in PAH mRNA (r.1199_2000ins1199+538_1199+562). Furthermore, the c.1199G>A mutation leads to the retention of an additional 17 nt in the PAH mRNA transcript (r.1199_2000ins1199+1_1199+17). These results expand the PAH genotypic spectrum and highlight that deep intronic analysis of PAH can improve genetic diagnosis in undiagnostic patients.

Peer review status:IN REVISION

08 Dec 2020Submitted to Human Mutation
15 Dec 2020Submission Checks Completed
15 Dec 2020Assigned to Editor
03 Jan 2021Reviewer(s) Assigned
22 Apr 2021Review(s) Completed, Editorial Evaluation Pending
23 Apr 2021Editorial Decision: Revise Major
01 Aug 20211st Revision Received
02 Aug 2021Submission Checks Completed
02 Aug 2021Assigned to Editor
11 Aug 2021Reviewer(s) Assigned
23 Aug 2021Review(s) Completed, Editorial Evaluation Pending
04 Sep 2021Editorial Decision: Revise Minor