ASN's Mission

To create a world without kidney diseases, the ASN Alliance for Kidney Health elevates care by educating and informing, driving breakthroughs and innovation, and advocating for policies that create transformative changes in kidney medicine throughout the world.

learn more

Contact ASN

1401 H St, NW, Ste 900, Washington, DC 20005


The Latest on X

Kidney Week

Please note that you are viewing an archived section from 2022 and some content may be unavailable. To unlock all content for 2022, please visit the archives.

Abstract: SA-PO562

Aberrant Splicing Affected by Single Nucleotide Variants Positioned at the Second and Third to the End of Exons in COL4A5 Gene

Session Information

  • Genetic Diseases: Diagnosis
    November 05, 2022 | Location: Exhibit Hall, Orange County Convention Center‚ West Building
    Abstract Time: 10:00 AM - 12:00 PM

Category: Genetic Diseases of the Kidneys

  • 1102 Genetic Diseases of the Kidneys: Non-Cystic


  • Okada, Eri, Kobe Daigaku, Kobe, Hyogo, Japan
  • Aoto, Yuya, Kobe Daigaku, Kobe, Hyogo, Japan
  • Horinouchi, Tomoko, Kobe Daigaku, Kobe, Hyogo, Japan
  • Yamamura, Tomohiko, Kobe Daigaku, Kobe, Hyogo, Japan
  • Nozu, Kandai, Kobe Daigaku, Kobe, Hyogo, Japan

As it has become more evident that male patients with X-linked Alport Syndrome show obvious genotype-phenotype correlation, it has been of great importance to clarify the impact on aberrant splicing caused by identified variants. We previously reported that single nucleotide variants (SNVs) at the last nucleotide of exons in COL4A5 gene highly cause aberrant splicing. It is generally considered that the 2nd and 3rd to the last nucleotides of exons can also play an important role in the first step of splicing process. The aim of the recent study is to investigate aberrant splicing affected by SNVs positioned at 2nd or 3rd to the last nucleotide of exons in COL4A5 gene.


We selected 8 candidate variants:6 from Human Gene Mutation Database Professional and 2 from our cohort. We performed in vitro splicing reporter assay and reverse transcription polymerase chain reaction (RT-PCR) for messenger RNA obtained from the patients if available.


Initial classification of the candidate variants was as follows: 3 nonsense, 2 missense and 3 synonymous. Splicing reporter assay and RT-PCR for messenger RNA revealed that 6 of 8 variants caused aberrant splicing. Four variants initially assessed as non-truncating variants were revealed to be truncating variants. One variant (No.7, c.685A>T, p.Lys229*) generated not only normal transcript but also aberrant transcript, which resulting in in-frame deletion.


We revealed that exonic SNVs positioned at the 2nd and 3rd to the last nucleotide of exon in COL4A5 gene can highly cause aberrant splicing. Minigene splicing assay is useful to confirm the effect of variants on aberrant splicing especially for genes that genotype-phenotype correlation is evident like COL4A5 gene to predict the patients’ prognosis.

Candidate variants and splicing outcome