Twelve exonic variants in the SLC12A1 and CLCNKB genes alter RNA splicing in a minigene assay

Identifying six single nucleotide variants in the COL17A1 gene that alter RNA splicing: database analysis and minigene assays

Collagen type XVII alpha 1 chain (COL17A1) is a protein in the collagen family crucial for maintaining the integrity of skin and epithelial tissues. It is also vital for enamel formation and plays a significant role in the differentiation of ameloblasts. Many studies have indicated that single nucleotide variants (SNVs) can disrupt normal splicing process of the pre-mRNA by altering various splicing regulatory signals. This study aimed to explore the potential impact of SNVs in COL17A1 geneon splicing events, with the ultimate aim of improving the prediction of disease prognosis. Here, we analyzed 703 SNVs including 446 exonic variants and 257 intronic variants in the COL17A1 gene using bioinformatics tools and identified candidate variants that may induce splicing alterations via minigene assays. Our study identified that, among eight candidate variants, six variants (c.1139 C > T, c.1834G > A, c.3198 C > T, c.202 + 6T > G, c.1222 + 4 A > G, c.3071-5G > A) induced splicing alterations by interfering with the recognition of classical splice sites or disrupting the ratio of exonic splicing enhancers/exonic splicing silencers, or both. This study emphasizes the necessity of assessing the effects of SNVs on at the mRNA level, aiding accurate characterization of COL17A1 variants and enabling the development of personalized treatment options.

Identified five variants in CFTR gene that alter RNA splicing by minigene assay

Background

Cystic fibrosis (CF) is a common monogenic multisystem disease caused primarily by variants in the CFTR gene. Emerging evidence suggests that some variants, which are described as missense, synonymous or nonsense variants in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process.

Methods

We analyzed 27 exonic variants in the CFTR gene utilizing bioinformatics tools and identified candidate variants that could lead to splicing changes through minigene assays. Ultimately, we selected eight candidate variants to assess their effects on pre-mRNA splicing. The numbering of DNA variants is based on the complementary DNA (cDNA)sequence of CFTR (Ref Seq NM_000492.4).

Results

This study assessed the impact of CFTR variants on exon splicing by combining predictive bioinformatics tools with minigene assays. Among the eight candidate single nucleotide alterations, five variants (c.488A>T,c.1117G>T, c.1209G>T, c.3239A>G and c.3367G>C) were identified as causing exon skipping.

Conclusion

Our study employed a minigene system, which offers great flexibility for assessing aberrant splicing patterns when patient mRNA samples are not accessible, to investigate the effects of exonic variants on pre-mRNA splicing. Our experimental outcomes highlight the importance of analyzing exonic variations at the mRNA level.

SLC12A1 variant c.1684+1 G>A causes Bartter syndrome type 1 by promoting exon 13 skipping

BACKGROUND

Bartter syndrome type 1, an autosomal recessive genetic disorder, is caused by pathogenic loss-of-function variants in the SLC12A1 gene. It is characterized by metabolic alkalosis and prenatal-onset polyuria leading to polyhydramnios.

METHODS

We identified pathogenic gene in a 12-day-old newborn boy with Bartter syndrome type 1 using whole-exome sequencing. Sanger sequencing validated the identified variants. A minigene assay was performed to investigate the effect of a novel splice site variant on pre-mRNA splicing.

RESULTS

We found a compound heterozygous variants in the SLC12A1 gene, consisting of a known pathogenic missense mutation (NM_000338: c.769 G>A; p.Gly257Ser) and a novel splice site variant (c.1684+1 G>A). In silico predictions and an in vitro minigene splicing assay demonstrated that the splicing variant c.1684+1 G>A abolished a consensus splice donor site of SLC12A1 intron 13, resulting in complete exon 13 skipping, translational frameshift, and premature termination codon, ultimately leading to loss of SLC12A1 function.

CONCLUSION

Using a cell-based in vitro assay, we revealed the aberrant effect of the pathogenic splicing variant SLC12A1 c.1684+1 G>A on pre-mRNA splicing. Our findings expand the gene mutation spectrum of Bartter syndrome type 1, providing a basis for genetic diagnosis and the development of genetic medicines.

Clinical, genetic characteristics and outcome of four Chinese patients with Bartter syndrome type 3: Further insight into a genotype-phenotype correlation

Aim

To investigate the characteristics of 4 Chinese patients with Bartter syndrome type 3 (BS Type 3).

Methods

The clinical data, genetic analysis, and outcome of four cases with Bartter syndrome type 3 were retrospectively summarised.

Results

Gene sequencing analysis showed that all children carried a compound heterozygous mutation in the CLCNKB gene and were diagnosed with BS type 3. All types of mutations were detected, including two missense mutations, one nonsense mutation, one small fragment deletion mutation, two large deletion mutations and one splice-site mutation. The splice-site mutation c.100 + 1 (IVS2) C > T was novel. Two cases carried large deletion mutations. The patients presented as classic BS with modest manifestations. The most common sign was growth retardation. There was no polyhydramnios or preterm delivery. All cases were treated with potassium chloride supplementation and indomethacin. During long-term follow-up, clinical symptoms and growth retardation improved significantly. Nephrocalcinosis or renal dysfunction was not observed.

Conclusion

The clinical manifestations of BS type 3 are mostly presented as cBS. Growth retardation is a common sign. BS type 3 had a good long-term prognosis. There were various types of mutations in the CLCNKB gene. Large deletions were the most common.

Three exonic variants in the PHEX gene cause aberrant splicing in a minigene assay

Background: X-linked hypophosphatemia (XLH, OMIM 307800) is a rare phosphorus metabolism disorder caused by PHEX gene variants. Many variants simply classified as missense or nonsense variants were only analyzed at the DNA level. However, growing evidence indicates that some of these variants may alter pre-mRNA splicing, causing diseases. Therefore, this study aimed to use bioinformatics tools and a minigene assay to ascertain the effects of PHEX variations on pre-mRNA splicing. Methods: We analyzed 174 variants in the PHEX gene described as missense or nonsense variants. Finally, we selected eight candidate variants using bioinformatics tools to evaluate their effects on pre-mRNA splicing using a minigene assay system. The complementary DNA (cDNA) sequence for the PHEX gene (RefSeq NM_000444.6) serves as the basis for DNA variant numbering. Results: Of the eight candidate variants, three were found to cause abnormal splicing. Variants c.617T>G p.(Leu206Trp) and c.621T>A p.(Tyr207*) in exon 5 altered the splicing of pre-mRNA, owing to the activation of a cryptic splice site in exon 5, which produced an aberrant transcript lacking a part of exon 5, whereas variant c.1700G>C p.(Arg567Pro) in exon 16 led to the activation of a cryptic splice site in intron 16, resulting in a partial inclusion of intron 16. Conclusion: Our study employed a minigene system, which has a great degree of flexibility to assess abnormal splicing patterns under the circumstances of patient mRNA samples that are not available, to explore the impact of the exonic variants on pre-mRNA splicing. Based on the aforementioned experimental findings, we demonstrated the importance of analyzing exonic variants at the mRNA level.

Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay

BACKGROUND

X-linked Alport syndrome (XLAS) is an inherited renal disease caused by rare variants of COL4A5 on chromosome Xq22. Many studies have indicated that single nucleotide variants (SNVs) in exons can disrupt normal splicing process of the pre-mRNA by altering various splicing regulatory signals. The male patients with XLAS have a strong genotype-phenotype correlation. Confirming the effect of variants on splicing can help to predict kidney prognosis. This study aimed to investigate whether single nucleotide substitutions, located within three bases at the 5' end of the exons or internal position of the exons in COL4A5 gene, cause aberrant splicing process.

METHODS

We analyzed 401 SNVs previously presumed missense and nonsense variants in COL4A5 gene by bioinformatics programs and identified candidate variants that may affect the splicing of pre-mRNA via minigene assays.

RESULTS

Our study indicated three of eight candidate variants induced complete or partial exon skipping. Variants c.2678G>C and c.2918G>A probably disturb classic splice sites leading to corresponding exon skipping. Variant c.3700C>T may disrupt splicing enhancer motifs accompanying with generation of splicing silencer sequences resulting in the skipping of exon 41.

CONCLUSION

Our study revealed that two missense variants positioned the first nucleotides of the 5' end of COL4A5 exons and one internal exonic nonsense variant caused aberrant splicing. Importantly, this study emphasized the necessity of assessing the effects of SNVs at the mRNA level.

Clinical Findings and Genetic Analysis of Nine Mexican Families with Bartter Syndrome

BACKGROUND

Bartter's syndrome (BS) is a group of salt-wasting tubulopathies characterized by hypokalemia, metabolic alkalosis, hypercalciuria, secondary hyperaldosteronism, and low or normal blood pressure. Loss-of-function variants in genes encoding for five proteins expressed in the thick ascending limb of Henle in the nephron, produced different genetic types of BS.

AIM

Clinical and genetic analysis of families with Antenatal Bartter syndrome (ABS) and with Classic Bartter syndrome (CBS).

METHODS

Nine patients from unrelated non-consanguineous Mexican families were studied. Massive parallel sequencing of a gene panel or whole-exome sequencing was used to identify the causative gene.

RESULTS

Proband 1 was homozygous for the pathogenic variant p.Arg302Gln in the SLC12A1 gene encoding for the sodium-potassium-chloride NKCC2 cotransporter. Proband 3 was homozygous for the nonsense variant p.Cys308* in the KCNJ1 gene encoding for the ROMK potassium channel. Probands 7, 8, and 9 showed variants in the CLCKNB gene encoding the chloride channel ClC-Kb: proband 7 was compound heterozygous for the deletion of the entire gene and the missense change p.Arg438Cys; proband 8 presented a homozygous deletion of the whole gene and proband 9 was homozygous for the nonsense mutation p.Arg595*. A heterozygous variant of unknown significance was detected in the SLC12A1 gene in proband 2, and no variants were found in SLC12A1, KCNJ1, BSND, CLCNKA, CLCNKB, and MAGED2 genes in probands 4, 5, and 6.

CONCLUSIONS

Genetic analysis identified loss-of-function variants in the SLC12A1, KCNJ1, and CLCNKB genes in four patients with ABS and in the CLCNKB gene in two patients with CBS.