Complex Transposon Insertion as a Novel Cause of Pompe Disease

Pompe disease (OMIM#232300) is an autosomal recessive lysosomal storage disorder caused by mutations in the GAA gene. According to public mutation databases, more than 679 pathogenic variants have been described in GAA, none of which are associated with mobile genetic elements. In this article, we report a novel molecular genetic cause of Pompe disease, which could be hardly detected using routine molecular genetic analysis. Whole genome sequencing followed by comprehensive functional analysis allowed us to discover and characterize a complex mobile genetic element insertion deep in the intron 15 of the GAA gene in a patient with infantile onset Pompe disease.

Founder Effects in Hereditary Hemorrhagic Telangiectasia

A founder effect can result from the establishment of a new population by individuals from a larger population or bottleneck events. Certain alleles may be found at much higher frequencies because of genetic drift immediately after the founder event. We provide a systematic literature review of the sporadically reported founder effects in hereditary hemorrhagic telangiectasia (HHT). All publications from the ACVRL1, ENG and SMAD4 Mutation Databases and publications searched for terms “hereditary hemorrhagic telangiectasia” and “founder” in PubMed and Scopus, respectively, were extracted. Following duplicate removal, 141 publications were searched for the terms “founder” and “founding” and the etymon “ancest”. Finally, 67 publications between 1992 and 2020 were reviewed. Founder effects were graded upon shared area of ancestry/residence, shared core haplotypes, genealogy and prevalence. Twenty-six ACVRL1 and 12 ENG variants with a potential founder effect were identified. The bigger the cluster of families with a founder mutation, the more remarkable is its influence to the populational ACVRL1/ENG ratio, affecting HHT phenotype. Being aware of founder effects might simplify the diagnosis of HHT by establishing local genetic algorithms. Families sharing a common core haplotype might serve as a basis to study potential second-hits in the etiology of HHT.

Identification of a Novel Frameshift Mutation in the TECTA Gene in an Iranian Family With Autosomal Nonsyndromic Hearing Loss

Hearing loss (HL) is one of the most frequent birth defects, and genetic factors contribute to the pathogenesis of the disorder in about half of the patients. In the present study, we performed whole-exome sequencing (WES) based on Next-generation sequencing (NGS) in an Iranian family with hereditary HL. Then, Sanger sequencing was used to verify the segregation of the variant recognized in affected family members. A novel homozygous frameshift variation, c.649-650insC, in TECTA was found in the family, which might lead to a truncated TECTA protein (p. Asn218Gln fsX31). Our findings propose that the homozygous TECTA-p.N218QfsX31 mutation is the pathogenic variant for ARNSHL. To the best of our knowledge, this mutation has not been described in patients with the HL phenotype and so far has not to be reported in any of the mutation databases. Our data expand the spectrum of mutations in the TECTA gene in nonsyndromic hearing loss.

Genomic analyses of all known putative familial hypercholesterolemia mutations showcase the value and limitations of public familial hypercholesterolemia mutation databases

Background/Introduction Familial hypercholesterolemia (FH) is genetically very heterogeneous and genomic and locus-specific public databases describing putative FH mutations are assumed to be of limited clinical utility because of classification errors. Purpose A description of all currently known publicly available putative FH mutations in order to determine the reliability of the classification of FH mutations described. Methods The LOVD and ClinVar databases were interrogated for the phenotype and genes of interest. Additional information on each variant was obtained using the Bioconductor toolset, gnomAD, and GETex. Results Currently know putative FH variants included 4,529 variants (97.2%) in the classical FH-genes LDLR (61%), PCSK9 (10%), and APOB (29%). Single nucleotide variants constituted 83% and 17% were copy number variants. Exonic variants contributed 78%, 14% of the variants were intronic, 7% large CNV, and 1% in upstream or downstream regions. Of the 4,529 variants, 45% were classified as pathogenic or likely-pathogenic (Fig. 1a). The ratio of exonic/intronic variants was 10.1 for pathogenic variants, 6.9 for likely pathogenic variants, 2.8 for likely benign and 1.4 for benign variants (p-value for class difference <2x10–6). For 502 frameshift mutations in exons that are particularly damaging, only 93.2% were classified as pathogenic or likely-pathogenic and 1.7% as benign or likely benign (Fig. 1b). Across 222 exon-covering deletions of >100 nucleotides, also particularly damaging, only 90.5% were classified as pathogenic or likely-pathogenic. Of the 4,529 variants, 1,561 (34.5%) were polymorphic in gnomAD. For these variants, the gnomAD sample size was on average 227420 (26102–282902). Of all 1,561 polymorphic variants in gnomAD 182 (11.6%) were classified as pathogenic or likely-pathogenic (Fig. 1c) and the variant frequency ranged from 10–4 to 10–6 (average 1.8x10–5), 43 with a frequency >1.8x10–5. Among variants found in gnomAD and classified as non-pathogenic, we observed ∼2000x higher frequencies (average 0.04). Of the 4,529 variants, 100 matched eQTLs or sQTLs in GTEx, none was annotated as pathogenic (Fig. 1d). Conclusion We review all currently known putative FH mutations with pathogenic or likely-pathogenic variants being mostly exonic. Highly damaging mutations are largely classified as pathogenic or likely-pathogenic, but up to 9% are not classified as pathogenic in the two public FH mutation databases. Assuming an FH population prevalence of 1/250 and 2000 pathogenic variants with the most frequent variant 10x more frequent than the average, we expect most pathogenic FH mutations at frequencies <2x10–5. We found 46 pathogenic or likely pathogenic variants to have a frequencies of >2x10–5 in the general population, evidence for misclassification. No pathogenic FH variant was found among GETEx eQTLs or sQTLs. Our data showcase the utility and weaknesses of the current public FH mutation databases. FH variants overview Funding Acknowledgement Type of funding source: Public hospital(s). Main funding source(s): Hôpitaux Universitaire de Genève - Fonds privés

Optimization of in silico tools for predicting genetic variants: individualizing for genes with molecular sub-regional stratification

Genes are unique in functional role and differ in their sensitivities to genetic defects, but with difficulties in pathogenicity prediction. This study attempted to improve the performance of existing in silico algorithms and find a common solution based on individualization strategy. We initiated the individualization with the epilepsy-related SCN1A variants by sub-regional stratification. SCN1A missense variants related to epilepsy were retrieved from mutation databases, and benign missense variants were collected from ExAC database. Predictions were performed by using 10 traditional tools with stepwise optimizations. Model predictive ability was evaluated using the five-fold cross-validations on variants of SCN1A, SCN2A, and KCNQ2. Additional validation was performed in SCN1A variants of damage-confirmed/familial epilepsy. The performance of commonly used predictors was less satisfactory for SCN1A with accuracy less than 80% and varied dramatically by functional domains of Nav1.1. Multistep individualized optimizations, including cutoff resetting, domain-based stratification, and combination of predicting algorithms, significantly increased predictive performance. Similar improvements were obtained for variants in SCN2A and KCNQ2. The predictive performance of the recently developed ensemble tools, such as Mendelian clinically applicable pathogenicity, combined annotation-dependent depletion and Eigen, was also improved dramatically by application of the strategy with molecular sub-regional stratification. The prediction scores of SCN1A variants showed linear correlations with the degree of functional defects and the severity of clinical phenotypes. This study highlights the need of individualized optimization with molecular sub-regional stratification for each gene in practice.

Mitchell-Riley Syndrome: A Novel Mutation in RFX6 Gene

A novel RFX6 homozygous missense mutation was identified in an infant with Mitchell-Riley syndrome. The most common features of Mitchell-Riley syndrome were present, including severe neonatal diabetes associated with annular pancreas, intestinal malrotation, gallbladder agenesis, cholestatic disease, chronic diarrhea, and severe intrauterine growth restriction. Perijejunal tissue similar to pancreatic tissue was found in the submucosa, a finding that has not been previously reported in this syndrome. This case associating RFX6 mutation with structural and functional pancreatic abnormalities reinforces the RFX6 gene role in pancreas development andβ-cell function, adding information to the existent mutation databases.