BackgroundNephrolithiasis (NL) is a complex multifactorial disease affecting up to 10%–20% of the human population and causing a significant burden on public health systems worldwide. It results from a combination of environmental and genetic factors. Hyperoxaluria is a major risk factor for NL.MethodsWe used a whole exome-based approach in a patient with calcium oxalate NL. The effects of the mutation were characterised using cell culture and in silico analyses.ResultsWe identified a rare heterozygous missense mutation (c.1519C>T/p.R507W) in the SLC26A6 gene that encodes a secretory oxalate transporter. This mutation cosegregated with hyperoxaluria in the family. In vitro characterisation of mutant SLC26A6 demonstrated that Cl−-dependent oxalate transport was dramatically reduced because the mutation affects both SLC26A6 transport activity and membrane surface expression. Cotransfection studies demonstrated strong dominant-negative effects of the mutant on the wild-type protein indicating that the phenotype of patients heterozygous for this mutation may be more severe than predicted by haploinsufficiency alone.ConclusionOur study is in line with previous observations made in the mouse showing that SLC26A6 inactivation can cause inherited enteric hyperoxaluria with calcium oxalate NL. Consistent with an enteric form of hyperoxaluria, we observed a beneficial effect of increasing calcium in the patient’s diet to reduce urinary oxalate excretion.

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Complete loss of the X-linked gene CASK causes severe cerebellar degeneration

Patel, Paras A; Hegert, Julia V; Cristian, Ingrid; Kerr, Alicia; LaConte, Leslie E W; Fox, Michael A; Srivastava, Sarika; Mukherjee, Konark

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108115pmid: 35149592

BackgroundHeterozygous loss of X-linked genes like CASK and MeCP2 (Rett syndrome) causes developmental delay in girls, while in boys, loss of the only allele of these genes leads to epileptic encephalopathy. The mechanism for these disorders remains unknown. CASK-linked cerebellar hypoplasia is presumed to result from defects in Tbr1-reelin-mediated neuronal migration.MethodHere we report clinical and histopathological analyses of a deceased 2-month-old boy with a CASK-null mutation. We next generated a mouse line where CASK is completely deleted (hemizygous and homozygous) from postmigratory neurons in the cerebellum.ResultThe CASK-null human brain was smaller in size but exhibited normal lamination without defective neuronal differentiation, migration or axonal guidance. The hypoplastic cerebellum instead displayed astrogliosis and microgliosis, which are markers for neuronal loss. We therefore hypothesise that CASK loss-induced cerebellar hypoplasia is the result of early neurodegeneration. Data from the murine model confirmed that in CASK loss, a small cerebellum results from postdevelopmental degeneration of cerebellar granule neurons. Furthermore, at least in the cerebellum, functional loss from CASK deletion is secondary to degeneration of granule cells and not due to an acute molecular functional loss of CASK. Intriguingly, female mice with heterozygous deletion of CASK in the cerebellum do not display neurodegeneration.ConclusionWe suggest that X-linked neurodevelopmental disorders like CASK mutation and Rett syndrome are pathologically neurodegenerative; random X-chromosome inactivation in heterozygous mutant girls, however, results in 50% of cells expressing the functional gene, resulting in a non-progressive pathology, whereas complete loss of the only allele in boys leads to unconstrained degeneration and encephalopathy.

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Consolidation of the clinical and genetic definition of a SOX4-related neurodevelopmental syndrome

Angelozzi, Marco; Karvande, Anirudha; Molin, Arnaud N; Ritter, Alyssa L; Leonard, Jacqueline M M; Savatt, Juliann M; Douglass, Kristen; Myers, Scott M; Grippa, Mina; Tolchin, Dara; Zackai, Elaine; Donoghue, Sarah; Hurst, Anna C E; Descartes, Maria; Smith, Kirstin;

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Mroczek, Magdalena; Longman, Cheryl; Farrugia, Maria Elena; Kapetanovic Garcia, Solange; Ardicli, Didem; Topaloglu, Haluk; Hernández-Laín, Aurelio; Orhan, Diclehan; Alikasifoglu, Mehmet; Duff, Jennifer; Specht, Sabine; Nowak, Kristen; Ravenscroft, Gianina; Chao, Katherine;

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Transcriptome-based variant calling and aberrant mRNA discovery enhance diagnostic efficiency for neuromuscular diseases

Hong, Sung Eun; Kneissl, Jana; Cho, Anna; Kim, Man Jin; Park, Soojin; Lee, Jeongeun; Woo, Sijae; Kim, Sora; Kim, Jun-Soon; Kim, Soo Yeon; Jung, Sungwon; Kim, Jinkuk; Shin, Je-Young; Chae, Jong-Hee; Choi, Murim

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108307pmid: 35387801

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Long-read sequencing to resolve the parent of origin of a de novo pathogenic UBE3A variant

Watson, Christopher Mark; Jackson, Lucy; Crinnion, Laura A; Bonthron, David T; Sheridan, Eamonn

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108314pmid: 35414530

Background The ever-increasing capacity of short-read sequencing instruments is driving the adoption of whole genome sequencing (WGS) as a universal approach to the diagnosis of rare genetic disorders. However, many challenging genomic regions remain, for which alternative technologies must be deployed in order to address the clinical question satisfactorily. Methods Here we report the use of long-read sequencing to resolve ambiguity over a suspected diagnosis of Angelman syndrome. Results Despite a normal chromosomal microarray result and methylation studies at the imprinted 15q11q13 locus, the continued clinical suspicion of Angelman Syndrome prompted trio WGS of the proband and his parents. A de novo heterozygous frameshift variant, c.2370_2373del (NM_130838.2) p.(Asp790Glufs*7), in UBE3A was identified. To determine the parental allele on which this variant arose, long-read sequencing of the flanking genomic region was performed. Comparison of the resulting haplotypes allowed us to determine that the pathogenic frameshift variant arose on the maternal allele, confirming a diagnosis of Angelman syndrome in this case. Conclusion Long-read nanopore sequencing provides significant clinical utility when assessing the parental origin of de novo variants.

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Targeted long-read sequencing identifies missing pathogenic variants in unsolved Werner syndrome cases

Miller, Danny E.; Lee, Lin; Galey, Miranda; Kandhaya-Pillai, Renuka; Tischkowitz, Marc; Amalnath, Deepak; Vithlani, Avadh; Yokote, Koutaro; Kato, Hisaya; Maezawa, Yoshiro; Takada-Watanabe, Aki; Takemoto, Minoru; Martin, George M.; Eichler, Evan E.; Hisama, Fuki M.; Oshima, Junko

2022 Journal of Medical Genetics

doi:

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Identifying the psychosocial predictors of ultraviolet exposure to the face in patients with xeroderma pigmentosum: a study of the behavioural factors affecting clinical outcomes in this genetic disease

Sarkany, Robert; Norton, Sam; Canfield, Martha; Morgan, Myfanwy; Foster, Lesley; Sainsbury, Kirby; Araujo-Soares, Vera; Wulf, Hans Christian; Weinman, John; Walburn, Jessica

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108323pmid: 35393336

BackgroundFor patients with xeroderma pigmentosum (XP), the main means of preventing skin and eye cancers is extreme protection against ultraviolet radiation (UVR), particularly for the face. We have recently developed a methodology for objectively measuring photoprotection behaviour (‘UVR dose to facial skin’) and have found that the degree of photoprotection varies greatly between patients with XP. We have previously identified factors affecting photoprotection behaviour in XP using a subjective measure of photoprotection. Here, we have used this objective methodology to identify the factors which determine photoprotection behaviour in XP.MethodsWe studied 29 psychological, social, demographic and clinical variables in 36 patients with XP. We have previously objectively measured UVR protection (by measuring the dose of UVR reaching the skin of the face over a 3-week period) in these patients. Here, we use linear mixed-effects model analysis to identify the factors which lead to the differences in degree of photoprotection observed in these patients.ResultsPsychosocial factors accounted for as much of the interindividual variation in photoprotection behaviour (29%) as demographic and clinical factors (24%). Psychosocial factors significantly associated with worse UVR protection included: automaticity of the behaviours, and a group of beliefs and perceptions about XP and photoprotection known to associate with poor treatment adherence in other diseases.ConclusionsWe have identified factors contributing to poor photoprotection in XP. Identifying these potentially reversible psychosocial features has enabled us to design an intervention to improve photoprotection in patients with XP, aiming to prevent skin and eye cancers in these patients.

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Clinical, biochemical and genetic characteristics of MOGS-CDG: a rare congenital disorder of glycosylation

Shimada, Shino; Ng, Bobby G; White, Amy L; Nickander, Kim K; Turgeon, Coleman; Liedtke, Kristen L; Lam, Christina T; Font-Montgomery, Esperanza; Lourenco, Charles M; He, Miao; Peck, Dawn S; Umana, Luis A; Uhles, Crescenda L; Haynes, Devon; Wheeler, Patricia G;

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Novel POLE mutations identified in patients with IMAGE-I syndrome cause aberrant subcellular localisation and protein degradation in the nucleus

Nakano, Tomohiro; Sasahara, Yoji; Kikuchi, Atsuo; Moriya, Kunihiko; Niizuma, Hidetaka; Niihori, Tetsuya; Shirota, Matsuyuki; Funayama, Ryo; Nakayama, Keiko; Aoki, Yoko; Kure, Shigeo

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108300pmid: 35534205

BackgroundDNA replisome is a molecular complex that plays indispensable roles in normal DNA replication. IMAGE-I syndrome is a DNA replisome-associated genetic disease caused by biallelic mutations in the gene encoding DNA polymerase epsilon catalytic subunit 1 (POLE). However, the underlying molecular mechanisms remain largely unresolved.MethodsThe clinical manifestations in two patients with IMAGE-I syndrome were characterised. Whole-exome sequencing was performed and altered mRNA splicing and protein levels of POLE were determined. Subcellular localisation, cell cycle analysis and DNA replication stress were assessed using fibroblasts and peripheral blood from the patients and transfected cell lines to determine the functional significance of POLE mutations.ResultsBoth patients presented with growth retardation, adrenal insufficiency, immunodeficiency and complicated diffuse large B-cell lymphoma. We identified three novel POLE mutations: namely, a deep intronic mutation, c.1226+234G>A, common in both patients, and missense (c.2593T>G) and in-frame deletion (c.711_713del) mutations in each patient. The unique deep intronic mutation produced aberrantly spliced mRNAs. All mutants showed significantly reduced, but not null, protein levels. Notably, the mutants showed severely diminished nuclear localisation, which was rescued by proteasome inhibitor treatment. Functional analysis revealed impairment of cell cycle progression and increase in the expression of phospho-H2A histone family member X in both patients.ConclusionThese findings provide new insights regarding the mechanism via which POLE mutants are highly susceptible to proteasome-dependent degradation in the nucleus, resulting in impaired DNA replication and cell cycle progression, a characteristic of DNA replisome-associated diseases.

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Nature Genetics Nucleic Acids Research Genetics Annual Review of Genetics Genomics Mammalian Genome Chromosome Research Journal of Genetics Russian Journal of Genetics

Tran-Mau-Them, Frédéric;

Barge-Schaapveld, Daniela Q C.M;

Ruivenkamp, Claudia AL;

Bökenkamp, Regina;

Vergano, Samantha;

Seco Moro, Maria Noelia;

Díaz de Bustamante, Aranzazu;

Ahrens-Nicklas, Rebecca C;

Lefebvre, Veronique

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108375pmid: 35232796

BackgroundA neurodevelopmental syndrome was recently reported in four patients with SOX4 heterozygous missense variants in the high-mobility-group (HMG) DNA-binding domain. The present study aimed to consolidate clinical and genetic knowledge of this syndrome.MethodsWe newly identified 17 patients with SOX4 variants, predicted variant pathogenicity using in silico tests and in vitro functional assays and analysed the patients’ phenotypes.ResultsAll variants were novel, distinct and heterozygous. Seven HMG-domain missense and five stop-gain variants were classified as pathogenic or likely pathogenic variant (L/PV) as they precluded SOX4 transcriptional activity in vitro. Five HMG-domain and non-HMG-domain missense variants were classified as of uncertain significance (VUS) due to negative results from functional tests. When known, inheritance was de novo or from a mosaic unaffected or non-mosaic affected parent for patients with L/PV, and from a non-mosaic asymptomatic or affected parent for patients with VUS. All patients had neurodevelopmental, neurological and dysmorphic features, and at least one cardiovascular, ophthalmological, musculoskeletal or other somatic anomaly. Patients with L/PV were overall more affected than patients with VUS. They resembled patients with other neurodevelopmental diseases, including the SOX11-related and Coffin-Siris (CSS) syndromes, but lacked the most specific features of CSS.ConclusionThese findings consolidate evidence of a fairly non-specific neurodevelopmental syndrome due to SOX4 haploinsufficiency in neurogenesis and multiple other developmental processes.

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108341pmid: 35393337

BackgroundBiallelic pathogenic variants in FXR1 have recently been associated with two congenital myopathy phenotypes: a severe form associated with hypotonia, long bone fractures, respiratory insufficiency and infantile death, and a milder form characterised by proximal muscle weakness with survival into adulthood.ObjectiveWe report eight patients from four unrelated families with biallelic pathogenic variants in exon 15 of FXR1.MethodsWhole exome sequencing was used to detect variants in FXR1.ResultsCommon clinical features were noted for all patients, which included proximal myopathy, normal serum creatine kinase levels and diffuse muscle atrophy with relative preservation of the quadriceps femoris muscle on muscle imaging. Additionally, some patients with FXR1-related myopathy had respiratory involvement and required bilevel positive airway pressure support. Muscle biopsy showed multi-minicores and type I fibre predominance with internalised nuclei.Conclusion FXR1-related congenital myopathy is an emerging entity that is clinically recognisable. Phenotypic variability associated with variants in FXR1 can result from differences in variant location and type and is also observed between patients homozygous for the same variant, rendering specific genotype–phenotype correlations difficult. Our work broadens the phenotypic spectrum of FXR1-related congenital myopathy.

BackgroundWhole-exome sequencing-based diagnosis of rare diseases typically yields 40%–50% of success rate. Precise diagnosis of the patients with neuromuscular disorders (NMDs) has been hampered by locus heterogeneity or phenotypic heterogeneity. We evaluated the utility of transcriptome sequencing as an independent approach in diagnosing NMDs.MethodsThe RNA sequencing (RNA-Seq) of muscle tissues from 117 Korean patients with suspected Mendelian NMD was performed to evaluate the ability to detect pathogenic variants. Aberrant splicing and CNVs were inspected to identify additional causal genetic factors for NMD. Aberrant splicing events in Dystrophin (DMD) were investigated by using antisense oligonucleotides (ASOs). A non-negative matrix factorisation analysis of the transcriptome data followed by cell type deconvolution was performed to cluster samples by expression-based signatures and identify cluster-specific gene ontologies.ResultsOur pipeline called 38.1% of pathogenic variants exclusively from the muscle transcriptomes, demonstrating a higher diagnostic rate than that achieved via exome analysis (34.9%). The discovery of variants causing aberrant splicing allowed the application of ASOs to the patient-derived cells, providing a therapeutic approach tailored to individual patients. RNA-Seq data further enabled sample clustering by distinct gene expression profiles that corresponded to clinical parameters, conferring additional advantages over exome sequencing.ConclusionThe RNA-Seq-based diagnosis of NMDs achieves an increased diagnostic rate and provided pathogenic status information, which is not easily accessible through exome analysis.

10.1136/jmedgenet-2022-108485

pmid:

35534204

BackgroundWerner syndrome (WS) is an autosomal recessive progeroid syndrome caused by variants in WRN. The International Registry of Werner Syndrome has identified biallelic pathogenic variants in 179/188 cases of classical WS. In the remaining nine cases, only one heterozygous pathogenic variant has been identified.MethodsTargeted long-read sequencing (T-LRS) on an Oxford Nanopore platform was used to search for a second pathogenic variant in WRN. Previously, T-LRS was successfully used to identify missing variants and analyse complex rearrangements.ResultsWe identified a second pathogenic variant in eight of nine unsolved WS cases. In five cases, T-LRS identified intronic splice variants that were confirmed by either RT-PCR or exon trapping to affect splicing; in one case, T-LRS identified a 339 kbp deletion, and in two cases, pathogenic missense variants. Phasing of long reads predicted all newly identified variants were on a different haplotype than the previously known variant. Finally, in one case, RT-PCR previously identified skipping of exon 20; however, T-LRS did not detect a pathogenic DNA sequence variant.ConclusionT-LRS is an effective method for identifying missing pathogenic variants. Although limitations with computational prediction algorithms can hinder the interpretation of variants, T-LRS is particularly effective in identifying intronic variants.

Bamshad, Michael J;

Nickerson, Deborah A;

Cushing, Tom;

Gates, Ryan;

Gomez-Ospina, Natalia;

Rosenzweig, Sergio D;

Adams, David R;

Gahl, William A;

Malicdan, May Christine V;

Raymond, Kimiyo M;

Freeze, Hudson H;

Wolfe, Lynne A

2022 Journal of Medical Genetics

doi: 10.1136/jmedgenet-2021-108177pmid: 35790351

PurposeTo summarise the clinical, molecular and biochemical phenotype of mannosyl-oligosaccharide glucosidase-related congenital disorders of glycosylation (MOGS-CDG), which presents with variable clinical manifestations, and to analyse which clinical biochemical assay consistently supports diagnosis in individuals with bi-allelic variants in MOGS.MethodsPhenotypic characterisation was performed through an international and multicentre collaboration. Genetic testing was done by exome sequencing and targeted arrays. Biochemical assays on serum and urine were performed to delineate the biochemical signature of MOGS-CDG.ResultsClinical phenotyping revealed heterogeneity in MOGS-CDG, including neurological, immunological and skeletal phenotypes. Bi-allelic variants in MOGS were identified in 12 individuals from 11 families. The severity in each organ system was variable, without definite genotype correlation. Urine oligosaccharide analysis was consistently abnormal for all affected probands, whereas other biochemical analyses such as serum transferrin analysis was not consistently abnormal.ConclusionThe clinical phenotype of MOGS-CDG includes multisystemic involvement with variable severity. Molecular analysis, combined with biochemical testing, is important for diagnosis. In MOGS-CDG, urine oligosaccharide analysis via matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry can be used as a reliable biochemical test for screening and confirmation of disease.