Journal of Medical Genetics最新文献

Rare variants in GRIA3, the gene encoding the GluA3 subunit of amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptors (AMPARs), are associated with defects in early brain development. Disease-causing variants are generally categorised as either loss of function (LoF) or gain of function (GoF) that appear to be linked to different symptoms. Here, we reported a de novo variant (N651D) that has mixed LoF and GoF in a female patient with a devastating developmental and epileptic encephalopathy, parkinsonism and cortical malformation. N651D is located in the M3 segment, which forms the filter pore of AMPAR tetramers. Interestingly, functional assays revealed that glutamate induced no currents in GluA3_N651D homomeric receptors, likely indicating an LoF effect. However, when co-expressed with the GluA2 subunit, the GluA2/A3_N651D heteromeric receptors showed slower deactivation and desensitisation curves, along with elevated non-desensitising steady-state currents, features typically observed in GoF variants. We speculate that variants with mixed LoF and GoF effects may lead to a more devastating phenotype compared with variants with GoF effects only.

Background: Hereditary haemorrhagic telangiectasia (HHT) and juvenile polyposis syndrome (JPS) can be caused by SMAD4 pathogenic variants. SMAD4 is a common transcription factor of the BMP/TGFβ signalling pathway. In this study, we developed a cell-based functional assay to address the pathogenicity of SMAD4 variants identified in the French HHT cohort.

Methods: SMAD4 variants were generated by site-directed mutagenesis. A functional assay was developed in a cell line that does not express SMAD4, and the different SMAD4 variants were tested for their capacity to activate the BMP and TGFβ response using luciferase reporter assays.

Results: Twelve SMAD4 variants were identified and studied. We were able to develop a robust functional assay for these variants. All the expressed variants resulted in loss of function (LOF) in response to BMP9 or TGFβ1 stimulation. SMAD4 variants within the MH2 domain expressed SMAD4 mutated proteins that were unable to hetero-oligomerise with other SMADs, which could explain their LOF. Finally, we tested primary human endothelial cells isolated from patients with HHT carrying SMAD4 heterozygous pathogenic variants and observed that they behaved like the control cells at rest or when stimulated with BMP9.

Conclusion: We developed a SMAD4 functional assay that allows discrimination between benign and pathogenic SMAD4 variants. We demonstrated that the underlying molecular mechanism of this pathogenicity is due mostly to a loss of hetero-oligomerisation. This assay will be transferable to clinical genetic laboratories and will improve the diagnosis of patients with HHT-JPS.

Background: Fabry disease is a progressive, X-linked lysosomal disorder caused by reduced or absent α-galactosidase A activity due to GLA variants. Females with Fabry disease often experience diagnostic delays and an underappreciated disease burden owing to their variable disease presentation and progression.

Methods: We conducted a post hoc analysis of all females from the clinical studies FACETS (NCT00925301) and ATTRACT (NCT01218659) and their open-label extensions, assessing baseline characteristics and long-term efficacy of migalastat regarding cardiac and renal function and Fabry-associated clinical events (FACEs).

Results: Overall, 60 females had a median migalastat exposure of 5.1 years. At baseline, the median age was 47 years with multiorgan involvement in 70.0% of females (≥2 organ systems: renal, cardiac, central nervous system, peripheral nervous system and gastrointestinal). At baseline, 21.7% of females had left ventricular hypertrophy (LVH). In multiorgan involvement and LVH subgroups, the median baseline estimated glomerular filtration rate (eGFR) was in chronic kidney disease stage 2. Annualised rate of change in left ventricular mass index remained below 1 g/m²/year regardless of LVH or eGFR category at baseline. Mean (SD) eGFR annualised change was -1.1 (2.8) mL/min/1.73 m² overall. Ten FACEs were reported in eight females, seven of whom had prior events. Seven FACEs were cardiac; the remaining three were cerebrovascular (all transient ischaemic attacks). The incidence of renal, cardiac and cerebrovascular events was 0, 24.9 and 10.7 events per 1000 patient-years, respectively.

Conclusion: These data show that females with Fabry disease experience considerable disease severity and burden and support the long-term efficacy of migalastat for the treatment of females.

Background: APC c.3920T>A; p.Ile1307Lys (I1307K), prevalent in individuals of Ashkenazi Jewish (AJ) origin, has been associated with a modestly increased colorectal cancer (CRC) risk. Clinical recommendations for I1307K heterozygotes vary across countries and expert groups, reflecting differences in population frequencies, modest risk estimates and limited data in non-AJ individuals.

Methods: We analysed UK Biobank data comprising 466 315 individuals (8944 with CRC), using genomic analysis to classify AJ and non-AJ ancestries.

Results: I1307K was identified in 7.1% of AJ and 0.08% of non-AJ white participants. No significant association with CRC was observed in AJ (OR: 0.71; 95% CI: 0.17 to 2.95) or non-AJ white individuals (OR: 1.05; 95% CI: 0.50 to 2.22). The previously established OR of 1.7-1.8 for AJ individuals lies within our 95% CI, indicating underpowered results due to limited CRC cases. No significant associations were detected for other cancers. Unbiased, adequately powered CRC case-control studies in non-AJ populations would require cohorts far larger than current resources for feasible analysis.

Conclusion: Clinical actionability of I1307K should prioritise risk stratification based on overall CRC risk and ancestry-dependent variant detection rates. However, management strategies need not differ by ancestry once a carrier is identified, as the biological impact of I1307K should be consistent across populations.

Purpose: The utility of genetic testing (GT) to guide cancer treatment, risk management and prevention has driven the demand for cancer genetic services. The global shortage of genetic counsellors (GCs) has led to the mainstreaming model. We evaluate the outcomes of the first GC-led service in Asia as a potential model for mainstreaming.

Methods: A retrospective review of patients managed by the service from 2013 to 2023 was conducted. Output data relevant to patient consultations, GT uptake and pathogenic variant carriers identified were extracted. A progress chart outlines the efforts made in addressing barriers, improving uptake and service delivery.

Results: Demand for GT has increased 18-fold. Uptake grew from 27% to an average of 81% from 2020, with no misconduct recorded. Carrier detection rate rose from 16% to 19-25% from 2015. The cost of GT has reduced significantly. Referral pathways for common hereditary cancer predisposition syndromes have been implemented. Support group events are held annually for carriers.

Conclusion: Our findings highlight the feasibility and success of a GC-led mainstreaming model that is safe and scalable. GCs are more time and cost-efficient than doctors in meeting GT demands while supporting carriers psychosocially. Expanding the GC workforce should be a priority in meeting the global demand for GT.

Background: Short-read genome sequencing (sr-GS) affords efficient and accurate characterisation of apparently balanced chromosomal rearrangement (ABCR) breakpoints except in 9%-11% of cases that remain undetectable.

Methods: Among 117 ABCR that we studied in patients with abnormal phenotype, 14 (11.9%) could not be detected by our current strategy including sr-GS, alignment against the GRCh38 reference genome and structural variant (SV) detection using Breakdancer V.1.4.5. These were all reciprocal translocations, 10 of which implicated constitutive heterochromatin, acrocentric short arms or pericentromeric regions. We re-aligned the sequencing data against the T2T-CHM13 V.2.0 reference genome and re-analysed them using five other SV callers (DELLY, GRIDSS, LUMPY, Manta and SvABA). In addition, 11 ABCRs were further characterised using FISH, linked-read sequencing, long-read sequencing or optical genome mapping, either isolated or combined.

Results: We were able to characterise the breakpoints at the bp level for 12 translocations and identify specific breakpoint patterns using Integrative Genome Viewer (IGV). In each translocation, at least one breakpoint involved highly repetitive elements such as alpha-satellites, segmental duplications, satellite repeats or other poorly mapped regions. For six out of 12 patients, one of the breakpoints could explain the phenotype either by gene disruption (CAMTA1, DYRK1A, NLGN4X) or position effect (BMP2, DIAPH2, SIX3).

Conclusion: Failure of sr-GS is due to highly repetitive genomic regions at SV breakpoints, either absent from the reference genome or not attributed to a unique position. The resolution of ABCRs is essential to patients' care since it allowed us to conclude to a pathogenic variant in 50% of patients.

RNU4ATAC is a non-coding gene involved in the minor spliceosome, and is mutated in a spectrum of syndromic skeletal disorders with recessive inheritance. Recently, biallelic RNU4ATAC pathogenic variants were detected in five patients presenting a complex syndromic phenotype and a brain malformation resembling the 'molar tooth sign' (MTS). This is the hallmark of Joubert syndrome (JS), a neurodevelopmental ciliopathy with multiorgan involvement.We reanalysed exome sequencing (ES) from 53 patients with JS, who lacked coding variants in known JS-associated genes. Four RNU4ATAC variants (n.16G>A, n.51G>A, n.13C>T and n.30G>A) were identified in compound heterozygosity in three probands, accounting for 5.6% of negative cases. All patients displayed the MTS and clinical features overlapping those of JS and RNU4ATAC-related skeletal disorders.These findings expand the phenotypic spectrum of RNU4ATAC-related disorders to include a complex neurological-skeletal ciliopathy phenotype, and highlight the relevance of ES reanalysis to uncover non-coding variants often undetected by conventional diagnostics.

Background: While AUTS2 is recognised as a pivotal neurodevelopmental gene, its role in skeletal morphogenesis has remained unexplored. We investigated the contribution of AUTS2 to radioulnar synostosis (RUS) and associated skeletal dysplasias through integrated molecular and phenotypic analyses of unrelated probands.

Methods: Comprehensive genetic profiling was performed on patients with RUS, including G-banding karyotyping, translocation breakpoint mapping via low-coverage whole-genome sequencing with PCR/Sanger validation, CNV detection using SNP array (Infinium OmniZhongHua-8) and qPCR, and exome sequencing followed by orthogonal Sanger confirmation.

Results: Four novel pathogenic AUTS2 variants were identified from four unrelated patients: a balanced translocation [46,XY,t(7;21)(q11.22;q21.1)] disrupting intron 5 (hg19:chr7:71,845,797); a heterozygous 2.99 Mb deletion (hg19:7q11.22[67,488,531-70,480,818]) spanning AUTS2 and flanking loci; and two de novo frameshift insertions (c.47_48insG; c.864_865insGGACTGTTGCAAAGAGCCA). All variants impaired the full-length AUTS2 transcript. Affected individuals exhibited RUS accompanied by additional skeletal anomalies (micrognathia, short stature, dysplasia of hip joint, tight heel cords) and other AUTS2 syndrome features. Notably, phenotypic overlap with Tsukahara syndrome (OMIM 603438) was observed, suggesting potential diagnostic continuity between these entities.

Conclusion: This study establishes AUTS2 as a critical regulator of skeletal development, with molecular disruptions directly linked to RUS pathogenesis and broader skeletal dysmorphogenesis.

Background: Inherited retinal diseases (IRDs) are a group of disorders often resulting in progressive vision loss, ultimately leading to blindness. A significant portion of their genetic causes remain unresolved, partly due to undiscovered disease-associated genes or variants. This study aimed to identify novel genetic links to IRDs.

Methods: All patients underwent comprehensive ophthalmological evaluation, including retinal imaging (fundus autofluorescence and macular optical coherence tomography) and electroretinogram testing. Whole exome sequencing and whole genome sequencing were performed on patients with clinically unsolved IRD, and data were analysed using an in-house pipeline to identify causal variants. Subsequently, Sanger sequencing was performed to confirm identified variants.

Results: Three unrelated patients from Europe, Middle East and East Asia were identified with unique late-onset retinal degeneration (Stargardt-like phenotype) associated with biallelic loss-of-function (LoF) variants in C19orf44 (HGNC: 26141), a gene of unknown function. The homozygous variant NM_032207.2:c.549_550del;p.Ser185Profs*2 was identified in two unrelated patients (European and Middle Eastern). Moreover, an East Asian patient had likely compound heterozygous LoF variants (NM_032207.2:c.1168C>T;p.Gln390*/c.976_977del;p.Leu326Lysfs*15).

Conclusions: Our findings establish C19orf44 as a novel disease-causing gene for IRD with Stargardt-like phenotype, expanding the genetic landscape of retinal degeneration.

Background: Autosomal dominant (AD) inheritance often arises through haploinsufficiency, dominant-negative or gain of function (GoF) effects, while autosomal recessive (AR) inheritance generally results from partial or complete loss of function (LoF). Yet, a subset of genes demonstrates both inheritance patterns. We aimed to curate a list of such 'AD/AR' genes and to propose additional candidates.

Methods: AD/AR genes were subcategorised based on genotype-phenotype correlations and disease mechanisms. Using bioinformatic analyses, we compared genes with AD, AR and AD/AR inheritance across various metrics, including gnomAD constraint values, exon count, protein length, quaternary structure and gene ontology terms. A machine learning-based metric was used to account for interdependence among features.

Results: Pathogenic variants in AD/AR genes can lead to distinct or similar phenotypes, depending on the molecular mechanism. AD/AR genes exhibit unique bioinformatic properties such as intermediate constraint scores, a combination of gene ontology terms, a greater average number of exons and an elevated propensity to form homomeric/heteromeric proteins. We identified homozygous LoF or clinically reported variants in nine genes previously classified as AD only.

Conclusion: Collectively, the data suggest that AD/AR genes possess distinctive features that likely underpin their dual inheritance modes. We propose nine candidate AD/AR genes and emphasise caution in filtering by inheritance type alone.