Prenatal Detection of Novel Compound Heterozygous Splice Site Variants of the KIAA0825 Gene in a Fetus with Postaxial Polydactyly Type A

Abstract

Postaxial polydactyly (PAP) is a common abnormality characterized by extra digits on hands and/or feet. To date, sequence variants in seven genes have been identified in non-syndromic PAP. In the present study, a fetus manifesting non-syndromic postaxial polydactyly type A (PAPA) was found by fetal ultrasonography. To better evaluate fetal prognosis, SNP array analysis and trio whole-exome sequencing (trio-WES) were performed to identify the underlying etiology. Although SNP array analysis revealed no abnormality, trio-WES identified compound heterozygous splice site variants in KIAA0825, c.-1-2A>T and c.2247-2A>G in intron 2 and intron 12, respectively. These two splice site variants were absent in control databases and were predicted to influence splicing by in silico analysis. To confirm the potential pathogenicity of the variants, in vitro splicing assays using minigene and RNA from peripheral leukocytes of the heterozygous parents were conducted. Minigene and RT-PCR assays demonstrated that the c.-1-2A>T variant led to the loss of the initiation codon, and the c.2247-2A>G variant mainly resulted in exon 13 skipping. Prenatal WES and subsequent functional studies are important approaches for defining the genetic etiology of fetuses with PAPA and are also essential for accurate genetic counseling and decision making. Taken together, this study expands the spectrum of KIAA0825 variations in PAPA patients and increases the knowledge of the molecular consequences of KIAA0825 splice site variants.

Case report: splicing effect of a novel heterozygous variant of the NUS1 gene in a child with epilepsy

“…Previous publications in the literature have reported that nonsense-mediated mRNA decay (NMD) can degrade transcripts containing premature termination codons (PTCs). However, a small fraction of transcripts can escape NMD and remain undegraded, with potential variations in outcomes observed in different mutant forms and/or cell types ( Yao et al, 2022 ; Chu et al, 2023 ; Munoz-Pujol et al, 2023 ; Zheng et al, 2023 ). Similar to c.691 + 1C>A, blood samples in our case of c.791 + 6T>G were collected to identify the consequent changes in mRNA.…”

“…To assess the functional consequence of our identified intronic variant, both in vivo (RNA-Seq/RT-PCR) and in vitro (minigene assay) analyses were performed. Patient blood sample is usually accessible for RNA-Seq/RT-PCR analysis of the whole transcriptome or certain genes of interest, which can be routine and quick to complete in diagnostic laboratories ( Fraiman et al, 2021 ; Yao et al, 2022 ; Chu et al, 2023 ; Munoz-Pujol et al, 2023 ; Zheng et al, 2023 ). However, tissue-specific expression can limit this in vivo application, since many genes may not be expressed at a detectable level in blood cells (even though this is not the case for NUS1 ).…”

Identification of GLI1 and KIAA0825 Variants in Two Families with Postaxial Polydactyly

“…To date, a total of six other pathogenic variants in KIAA0825 have been reported in subjects with PAP. Four pathogenic variants [p.(Gln198Thrfs*21), p.(Lys725*), p.(Leu17Ser), and p.(Cys48Serfs*28)] were reported in Pakistani families [ 7 , 8 , 31 ] as well as two splice site variants [c.-1-2A>T and c.2247-2A>G] in a Chinese fetus ( Table 3 ) [ 32 ].…”

Genetic overview of postaxial polydactyly: Updated classification

“…Yao et al 28 reported a fetus manifesting non‐syndromic PAP‐A was found by fetal ultrasonography. They performed SNP array analysis and trio whole‐exome sequencing (trio‐WES) and identified compound heterozygous splice site variants (c.‐1‐2A>T [intron 2] and c.2247‐2A>G [intron 12]) in the KIAA0825 gene, respectively.…”

“…They performed SNP array analysis and trio whole‐exome sequencing (trio‐WES) and identified compound heterozygous splice site variants (c.‐1‐2A>T [intron 2] and c.2247‐2A>G [intron 12]) in the KIAA0825 gene, respectively. After performing minigene splice assay and RTPCR assays they showed that the c.‐1‐2A>T variant led to the loss of the initiation codon, and the c.2247‐2A>G variant resulted in skipping of exon 13 28 …”