Clinical Features and Mutation Analysis of the SMARCAD1 Gene in a Family with Basan Syndrome and a Literature Review / 罕见病研究

  Objective  To summarize the clinical features of a family with Basan syndrome and to analyze mutation of the SMARCAD1 gene.  Methods  The Basan family was diagnosed at Dermatology Hospital, Southern Medical University in 2022. Backgroud data was collected, and clinical and genetic characteristics were analyzed. Meanwhile, a retrospective analysis of features and associated genetic mutations reported in all patients with Basan syndrome was conducted.  Results  A total of 18 patients with Basan syndrome were identified, including 9 males and 9 females. All 18 patients had no fingerprints at birth (18/18, 100%), and some patients had knuckle pads, palmoplantar hyperkeratosis, nail atrophy, nail separation, and longitudinal nail ridges. Symptoms vary in severity. At the same time, it was found that c.-10+1G > T (as well as c.378+1G > T)mutations appeared on the intron 1 of the SMARCAD1 (NM_020159.5) gene in 7 patients, resulting in abnormal splicing.  Conclusions  This article provides help for the early diagnosis of Basan syndrome and helps to improve the diagnosis and differentiation level of clinicians.

Deciphering the pathogenicity of COL4A4 heterozygous splicing mutations and the genotype-phenotype correlation in autosomal dominant Alport syndrome / 中华肾脏病杂志

Objective:Through the investigation of the pathogenicity of COL4A4 heterozygous splicing mutations and the genotype-phenotype correlation in autosomal dominant Alport syndrome (ADAS), to better understand the impact of COL4A4 heterozygous splicing mutations on ADAS. Methods:The study was a case series analysis. Patients from 5 ADAS families with COL4A4 heterozygous splicing mutations detected by whole exome sequencing were recruited by three hospitals. In vivo transcriptional analysis and/or in vitro minigene splicing assay were conducted to determine the splicing patterns and assess the pathogenicity of COL4A4 heterozygous splicing mutations. Results:In the five ADAS pedigrees carrying COL4A4 heterozygous splicing mutations, four novel ADAS splicing patterns were described. In pedigree 1-4, most patients presented with continuous hematuria or/and microalbuminuria. Otherwise,the proband in pedigree 4 presented with macroalbuminuria and the proband in pedigree 1 had progressed to chronic kidney disease stage 2 at the age of 70 years old. In pedigree 5, all patients developed end-stage renal disease between 28 and 41 years old. c.735+3A>G detected in pedigree 1 and pedigree 2 and c.694-1G>C detected in pedigree 3 both led to exon 12 skipping in COL4A4, resulting in 42 nucleotides in-frame deletion (c.694_735del). c.2056+3A>G detected in pedigree 4 led to COL4A4 exon 26 skipping, which caused in-frame deletion of 69 nucleotides (c.1988_2056del). c.2716+5G>T detected in pedigree 5 led to a 360 nucleotides large in-frame deletion, including 100 bp sequence at the 3'end of exon 29,the whole sequence of exon 30 and 89 bp sequence at the 5'end of exon 31 (c.2446_2805del). Conclusions:Renal prognosis differs significantly for patients with small in-frame deletions versus large in-frame deletion splicing abnormalities. Determination of the pathogenicity and the splicing patterns of COL4A4 heterozygous splicing mutations using in vivo and in vitro transcriptional analysis may provide renal prognostic information.

A novel mutation in the WNT6 gene of congenital tooth agenesis / 口腔疾病防治

Objective @#This article explores the relationship between congenital tooth agenesis and related gene mutations, providing a reference for early diagnosis of the disease.@*Methods @# Clinical and radiographic examinations of a rare case of congenital tooth agenesis were conducted to evaluate the abnormal morphology and quantity of the teeth, as well as the overall health of the patient. Bidirectional sequencing of the PAX9 and MSX1 genes and whole-exome sequencing were conducted to identify potential genetic abnormalities. Sanger sequencing of the newly discovered mutation site was performed on the proband's son. Subsequently, the impacts of the mutations were evaluated through computational tools and a cell-based gene transfection assay. @*Results @#This is a rare case of tooth agenesis characterized by a congenitally missing first molar, a second molar with one single root and a supernumerary second premolar in the right mandibular dentition. The c.717 C>C/T in PAX9 is synonymous. The c.119C>G in MSX1 is a missense mutation predicted to be “benign” by Polyphen. Through whole-exome sequencing, we found a novel mutation, c.637-7 C>A in intron 3 of the WNT6 gene, which is predicted by MAXENT to influence the splicing of mRNA. Both the proband and his son carry this mutation. A cell-based gene transfection assay demonstrated that it did not alter the mRNA splicing of WNT6. @* Conclusion @#The interaction between single nucleotide polymorphisms may contribute to congenital tooth agenesis.

Exon 35 skipping of FBN1 caused by c.4336G>A mutation may lead to Marfan syndrome / 中华检验医学杂志

Objective:To investigate the genetic etiology of a Marfan syndrome pedigree, and the impact of c.4336G>A variant on the splicing process of FBN1 gene.Methods:The proband was admitted to the Department of Cardiovascular Surgery of Xijing Hospital due to thoracic aortic aneurysm and dissection in August 2019. Multiplex PCR and next generation sequencing technology were used to detect 15 genes associated with hereditary aortic diseases in the proband. Then the pathogenic sites were further verified by Sanger sequencing, and above examinations were also performed among the family members of the proband. The effect of the mutation on mRNA splicing was predicted by splicing prediction software. RNAs from peripheral blood cells of the proband and the healthy person were extracted, and the effect of the mutation on mRNA splicing was verified by reverse transcription PCR and Sanger sequencing. The pathogenicity was analyzed by the recommendations from the American College of Medical Genetics (ACMG).Results:The gene panel detected a missense mutation of FBN1 gene (c.4336G>A) in the proband. Sanger sequencing results were consistent with that of panel. Sanger sequencing results showed that 4 family members were carriers of the same variant, and 3 out of the 4 family members presented signs of thoracic aortic aneurysm and dissection. The dbscSNV_ada_score and dbscSNV_rf_score software predicted that this mutation would lead to the occurrence of abnormal splicing of mRNA. The skipping of exon 35 was verified in the subsequent examinations by reverse transcription PCR and Sanger sequencing. The variant was classified as"pathogenic"according to ACMG guideline.Conclusion:FBN1 c.4336G>A mutation can cause the skipping of exon 35, and this might be the genetic mechanistic of severe cardiovascular abnormalities observed in this Marfan syndrome pedigree.

Novel mutation c.1210-3C > G in cis with a poly-T tract of 5T affects CFTR mRNA splicing in a Chinese patient with cystic fibrosis / 医学前沿

Cystic fibrosis (CF) is a rare autosomal recessive disease with only one pathogenic gene cystic fibrosis transmembrane conductance regulator (CFTR). To identify the potential pathogenic mutations in a Chinese patient with CF, we conducted Sanger sequencing on the genomic DNA of the patient and his parents and detected all 27 coding exons of CFTR and their flanking intronic regions. The patient is a compound heterozygote of c.2909G > A, p.Gly970Asp in exon 18 and c.1210-3C > G in cis with a poly-T of 5T (T5) sequence, 3 bp upstream in intron 9. The splicing effect of c.1210-3C > G was verified via minigene assay in vitro, indicating that wild-type plasmid containing c.1210-3C together with T7 sequence produced a normal transcript and partial exon 10-skipping-transcript, whereas mutant plasmid containing c.1210-3G in cis with T5 sequence caused almost all mRNA to skip exon 10. Overall, c.1210-3C > G, the newly identified pathogenic mutation in our patient, in combination with T5 sequence in cis, affects the CFTR gene splicing and produces nearly no normal transcript in vitro. Moreover, this patient carries a p.Gly970Asp mutation, thus confirming the high-frequency of this mutation in Chinese patients with CF.

Pathogenicity evaluation and splicing correction of COL4A5 splice mutation in X-linked Alport syndrome / 中华肾脏病杂志

Objective:To analyze the splicing mutation site of COL4A5 gene in a family with X-linked dominant Alport syndrome and explore the possibility of exon specific U1 small nuclear RNA (snRNA) gene therapy. Methods:The clinical data of the proband and family members of Alport syndrome were collected, and the gene mutations in the whole exon of a series of nephropathy genes in the proband were detected by high-throughput sequencing. The splice site changes and pathogenicity caused by COL4A5 c.546+5G>A mutation were analyzed by online software. Minigene experiment was used to verify and analyze the effect of COL4A5 gene mutation site c.546+5G>A in the proband of Alport syndrome family, and transient transfection and introduction of modified U1 snRNA to correct splicing mutation. Results:The results of gene sequencing showed that there was a hemizygous variation of COL4A5 gene in the proband and his half brother, and the variation site was c.546+5G>A. The results of online software for analyzing the pathogenicity of splice variation showed that the original donor splicing site could not be detected after mutation, suggesting that there was a great possibility of affecting splicing. The abnormal splicing mode of COL4A5 gene with c.546+5G>A mutation—deletion of exon 9 was verified by hybridized small gene detection. The abnormal splicing mutation could be partially corrected by the modified U1 snRNA. The correction ratios of ExSpeU1 (MT), ExSpeU1(E9+1), ExSpeU1(E9+9) and ExSpeU1(E9+11) to exon 9 deletion caused by c.546+5G>A were 0, 43.81%, 52.09% and 48.12%, respectively. Conclusions:The pathogenicity of the new splicing mutation of COL4A5 is verified, and the modified U1 snRNA can partially correct the abnormal splicing.

A novel splicing mutation identified in a Chinese family with Alport syndrome and analysis of its pathogenicity / 医学研究生学报

Objective The purpose of this study was to identify a pathogenic variant in a Chinese family with Alport syndrome and analyze the pathogenicity of the variant. Methods Using targeted region capture and high-throughput sequencing technology, we identified the genetic variant of the proband with Alport syndrome, verified the variant in the family members by Sanger sequencing, and analyzed its influence on the pre-mRNA splicing process by in vitro minigene assay. Results A heterozygous variant c.2767G>T (p.Gly923Cys) was identified as a novel variant in exon 32 of the COL4A5 gene in the proband, which was confirmed by Sanger sequencing to be cosegregated with disease in the family. The minigene assay demonstrated that the c.2767G>T variant induced deletion of exon 32 of the COL4A5 gene. Conclusion A novel COL4A5 mutation was identified by targeted region capture and high-throughput sequencing, which has enriched the gene mutation spectrum of Alport syndrome. The exonic mutation c.2767G>T confirmed to be a splicing mutation by in vitro minigene assay, which may lead to a deeper insight into the molecular pathogenesis of Alport syndrome.

The clinical characteristics and molecular pathogenesis of a variant Glanzmann’s thrombasthenia-like pedigree / 中华血液学杂志

Objective@#To review the clinical characteristics of a pedigree with inherited hemorrhagic disease to explore its molecular pathogenesis.@*Methods@#The clinical data of the pedigree with inherited hemorrhagic disease were collected. After extracting DNA, next generation sequencing was utilized to detect the potential gene mutation. The changes of RASGRP2 transcript of this proband and his parents were detected using RT-PCR to compare with normal control.@*Results@#The phenotype of the proband in this pedigree with inherited platelet dysfunction and bleeding disorder was similar to variant Glanzmann’s thrombasthenia, the maximum aggregations of platelet in response to the physiological agonists including ADP, epinephrine and arachidonic acid were significantly lower, leading to severe spontaneous mucosal bleeding. Integrin αIIbβ3 gene mutation was not detected, but another gene mutation RASGRP2 IVS3-1 stood out. The mutation was homozygous in the proband and heterozygosis in both of his parents. Two transcript types were detected in the proband, without transcripts coding functional RASGRP2 protein, however, his parents had functional transcripts and abnormal transcripts, with the normal transcripts in the majority.@*Conclusions@#The RASGRP2 IVS3-1 gene mutation was responsible for the inherited hemorrhagic disease. The RASGRP2 IVS3-1 gene mutation led to abnormal alternative splicing, without formation of functional RASGRP2 protein. The RASGRP2 protein is at the nexus of calcium-dependent platelet activation and hemostasis after damage of blood vessels. Spontaneous mucosal bleeding was a result of the lack of the functional RASGRP2 protein. This was the first report of RASGRP2 gene mutation resulting in bleeding disorder in China, and also the first report of the mutation type of RASGRP2 IVS3-1.

An unique exonic splicing mutation in the CYPI7AI gene as the cause of steroid 17α-hydroxylase deficiency / 中华内分泌代谢杂志

Objective To analyze CYP17A1 gene mutation in a patient with 46,XY disordered sex development and to explore the possible influence on the phenotype of the patient.Methods Eight exons of CYP17AI gene in the patient and her parents were amplified and directly sequenced.In order to construct Mini-gene system,PCR fragments containing wildtype and mutant splicing sites were inserted in expression vector,and then transfected into cells.RT-PCR was used to observe the influence of splicing site mutation.Wildtype and aberrant splicing CYP17A1 cDNA expression plasmids were constructed and transfected into cells respectively,and CYP17A1 enzyme activity was tested in vitro.Results Mutation analysis revealed compound heterozygous CYP17A1 mutations,with Y329fs in one allele and a synonymous substitution( c.1263G＞A:GCG＞GCA) in another allele.In vitro analysis showed that the synonymous substitution induced a novel splicing site,which resulted in aberrant splicing of CYP17A1 mRNA and lacked six or seven amino acids after 415 in splicing product.In vitro transfection and enzyme activity experiment showed that the aberrant splicing product abolished the enzyme activity completely.However,this mutation did not completely influence splicing.The patient also had a part of normal splicing product,which was a coincidence to the phenotype of the patient.Conclusion This is the first description of an exonic splicing mutation in CYP17A1 relevant to the 17ot-hydroxylase deficiency phenotype.The functional study of the aberrant splicing variant has been initiated.

A novel splicing mutation in intron 2 of DSPP gene in a family with dentinogenesis imperfecta type Ⅱ / 临床检验杂志

Objective To report a familial dentinogenesis imperfecta type Ⅱ (DGI type Ⅱ) with a novel splicing mutation in DSPP (dentin sialophosphoprotein) gene.Methods Based on the result of linkage analysis performed previously to map the candidate gene DSPP in the family, the promoter,the first four exons and exon-intron boundaries of DSPP were directly sequenced for the members of the DGI type Ⅱ family. Denaturing high performance liquid chromatography (DHPLC) analysis was performed to confirm the results of sequencing.Results A novel splicing mutation of 23 bp deletion in intron 2 of DSPP gene was identified by DNA sequence analysis. The mutation changed acceptor site sequence from CAG to AAG, and might result in functional abolition of possible branch point site in intron 2. DHPLC result was consistent with that of sequencing. The mutation may be identified in all affected individuals, but not found in normal members of the family and 50 controls.Conclusion These results suggest the deleted mutation of DSPP gene causes DGI type Ⅱ in the family. The mutation has not been reported before.