Promoter Deletion Leading to Allele Specific Expression in a Genetically Unsolved Case of Primary Ciliary Dyskinesia

• Published in: American journal of medical genetics. Part A Vol. 197; no. 2; pp. e63880 - n/a
• Main Authors: Beaman, M. Makenzie, Yin, Weining, Smith, Amanda J., Sears, Patrick R., Leigh, Margaret W., Ferkol, Thomas W., Kearney, Brendan, Olivier, Kenneth N., Kimple, Adam J., Clarke, Shannon, Huggins, Erin, Nading, Erica, Jung, Seung‐Hye, Iyengar, Apoorva K., Zou, Xue, Dang, Hong, Barrera, Alejandro, Majoros, William H., Rehder, Catherine W., Reddy, Timothy E., Ostrowski, Lawrence E., Allen, Andrew S., Knowles, Michael R., Zariwala, Maimoona A., Crawford, Gregory E.
• Format: Journal Article
• Language: English
• Published: Hoboken, USA John Wiley & Sons, Inc 01.02.2025; Wiley Subscription Services, Inc
• Subjects: 3' Untranslated regions; 5' Untranslated regions; Alleles; Autosomal recessive inheritance; Ciliary Motility Disorders - genetics; Ciliary Motility Disorders - pathology; DNA sequencing; Dyskinesia; Exome Sequencing; Female; Gene deletion; gene regulation; Genetic disorders; Genetic diversity; Genetics; Genomes; Genomic analysis; Humans; Kartagener Syndrome - diagnosis; Kartagener Syndrome - genetics; Kartagener Syndrome - pathology; long‐read sequencing; Male; nanopore; non‐coding variant; Pedigree; Primary ciliary dyskinesia; Promoter Regions, Genetic - genetics; Ribonucleic acid; RNA; RNA sequencing; Sequence Deletion - genetics; Whole genome sequencing; RNA sequencing; non‐coding variant; long‐read sequencing; gene regulation; nanopore; primary ciliary dyskinesia
• ISSN: 1552-4825; 1552-4833; 1552-4833
• DOI: 10.1002/ajmg.a.63880

ABSTRACT Variation in the non‐coding genome represents an understudied mechanism of disease and it remains challenging to predict if single nucleotide variants, small insertions and deletions, or structural variants in non‐coding genomic regions will be detrimental. Our approach using complementary RNA‐seq and targeted long‐read DNA sequencing can prioritize identification of non‐coding variants that lead to disease via alteration of gene splicing or expression. We have identified a patient with primary ciliary dyskinesia with a pathogenic coding variant on one allele of the SPAG1 gene, while the second allele appears normal by whole exome sequencing despite an autosomal recessive inheritance pattern. RNA sequencing revealed reduced SPAG1 transcript levels and exclusive allele specific expression of the known pathogenic allele, suggesting the presence of a non‐coding variant on the second allele that impacts transcription. Targeted long‐read DNA sequencing identified a heterozygous 3 kilobase deletion of the 5′ untranslated region of SPAG1, overlapping the promoter and first non‐coding exon. This non‐coding deletion was missed by whole exome sequencing and gene‐specific deletion/duplication analysis, highlighting the importance of investigating the non‐coding genome in patients with “missing” disease‐causing variation. This paradigm demonstrates the utility of both RNA and long‐read DNA sequencing in identifying pathogenic non‐coding variants in patients with unexplained genetic disease.