Journal of Human Genetics最新文献

Non-invasive prenatal testing (NIPT) is a screening method that detects fetal chromosomal trisomies from cell-free DNA in maternal blood. Because NIPT uses whole-genome sequencing with next-generation sequencing for data processing, it can also detect maternal genomic information. Although most copy number variations (CNVs) are benign, some have been reported to be associated with pathological phenotypes and are attracting increasing attention. However, most CNV studies have been conducted in Western populations, and large-scale studies in Japanese cohorts remain scarce. This study represents the first multicenter, large-scale cohort investigation of maternal CNVs in Japanese pregnant women. We analyzed 46,082 participants to establish a reliable threshold for maternal CNV detection and to evaluate their clinical significance. Maternal CNVs were validated using array comparative genomic hybridization, and receiver operating characteristic curve analysis identified 0.8 Mbp as the minimum threshold achieving 100% specificity. Applying this criterion, maternal CNVs were identified in 2907 cases (6.3%), with the most frequent being a duplication at chr8: 3,842,478-6,092,478 (hg38, allele frequency 2.67%). Comparison with public genomic databases, including the Tohoku Medical Megabank Organization (ToMMo) and the Genome Aggregation Database (gnomAD), confirmed that all CNVs detected in this study had been previously reported, with particularly high concordance in ToMMo. Notably, several very rare CNVs were also identified. These findings demonstrate that NIPT can reliably detect maternal CNVs ≥0.8 Mbp, which appear to represent benign genomic variants that are unlikely to affect fertility or early miscarriage.

Spinocerebellar ataxia type 41 (SCA41) is a rare autosomal dominant cerebellar ataxia caused by mutations in the transient receptor potential canonical 3 (TRPC3) gene. We report a case of a patient with SCA41 whose clinical manifestations were initially suspected to be multiple system atrophy cerebellar-type (MSA-C). Whole-exome sequencing (WES) revealed a c.1955A>G (p.K652R) mutation in the TRPC3 gene of this patient. After treatment with transcranial magnetic stimulation and rehabilitation training, the patient reported a slight improvement in unsteady gait compared with before. This is the first report of SCA41 caused by the c.1955A>G variant in the TRPC3 gene, which expands the mutation spectrum of the TRPC3 gene. Clinicians should have sufficient awareness of SCA41, as SCA and MSA-C share overlapping clinical phenotypes and imaging features, which may easily lead to misdiagnosis, and genetic testing plays a crucial role in differentiating between the two disorders.

Recent studies have revealed de novo or germline-derived GNAS-Gsα variants with constitutive ligand-independent gain-of-function (GOF) effects on specific G-protein-coupled receptor signalings in patients with nephrogenic syndrome of inappropriate antidiuresis (NSIAD), osteolytic bone disorder with metaphyseal dysplasia, and peripheral precocious puberty. We encountered a Japanese girl with NSIAD and osteolytic bone disorder with metaphyseal dysplasia. Whole genome sequencing identified a de novo ″likely pathogenic″ heterozygous GNAS-Gsα missense variant (NM_000516.7:c.163 A > G:p.(Thr55Ala)) which occurred on the paternally inherited allele. Luciferase assays for p.Thr55Ala showed ligand-independent GOF effects on AVPR2 and PTH1R signalings, and a ligand-dependent loss-of-function (LOF) effect on PTH1R signaling. Protein structural analysis for p.Thr55Ala indicated disruption of the hydrogen bond between p.Thr55 side chain and the α-phosphate group of the bound nucleotide in both GDP-bound inactive form and GTP-bound active form and resultantly reduced affinity of the variant-positive Gsα protein for both GDP and GTP, consistent with the ligand-independent GOF and ligand-dependent LOF effects. The results, in conjunction with the previous findings, indicate that GNAS-Gsα variants with constitutive GOF effects cause clinically distinctive congenital rare disorders including NSIAD and characteristic bone disorder.

The importance of 5'-untranslated region (5'-UTR) variants in genetic diseases has become increasingly recognized. However, systematic frameworks for interpreting their pathogenic mechanisms remain underdeveloped. We performed genome sequencing (GS) or reanalyzed exome sequencing (ES) data from patients with neurodevelopmental disorders in whom no pathogenic variants had previously been identified, and searched for variants affecting upstream open reading frames (uORFs) in the 5'-UTR using UTRannotator, a tool for annotating 5'-UTR variants. We identified one patient with a maternally inherited single nucleotide duplication upstream of ATRX (c.-138dup), which is predicted to result in the formation of an out-of-frame uORF overlapping the coding sequence (CDS). The patient exhibited the core features of ATRX-related disorders. RNA sequencing of urine-derived cells (UDCs) revealed reduced ATRX expression in the patient. Luciferase reporter assays demonstrated that wild-type and mutant ATRX 5'-UTR sequences conferred significantly increased and decreased luciferase activity compared with the parental pGL3-promoter vector, respectively, suggesting that the c.-138dup variant may disrupt an enhancer-like regulatory element and impair translation. We also identified another patient with a de novo single nucleotide variant upstream of POU3F3 (c.-303C>A), which introduces a novel uORF overlapping the CDS in-frame. This patient showed phenotypes consistent with POU3F3-related disorder. Although immunoblotting using UDCs revealed no elongated POU3F3 proteins, the luciferase assay showed reduced activity with mutant 5'-UTR compared to the wild-type. Our study demonstrates that integrating GS or ES with UTRannotator is useful for identifying candidate 5'-UTR variants; however, the potential impact of predicted non-coding variants still requires careful experimental evaluation.

Lipocalin-2 (LCN2) level, leukocyte count (LC), and renal function are key biomarkers linked to inflammation and metabolism. We aimed to explore the genetic determinants, causal associations, and long-term outcome effects of LCN2 levels. Phenotypic associations, genome-wide association studies (GWASs), linkage disequilibrium score regression (LDSC), and Mendelian randomization (MR) analyses for genetic correlation and causal associations between LCN2, LC, and estimated glomerular filtration rate (eGFR) were performed in 8208, 117,666, and 117,666 Taiwan Biobank participants, respectively. Long-term outcome analyses were performed for LCN2 in 481 patients with coronary artery disease (CAD). Elevated LCN2 levels were associated with older age, male sex, and altered metabolic parameters. GWAS of LCN2 levels identified genome-wide significant loci on LCN2, GSDMA, and MYB. LDSC revealed a limited number of shared loci between LCN2 level, LC and eGFR rather than broad polygenic overlap. MR analyses showed weighted genetic risk scores for LC and eGFR were significantly associated with LCN2 levels, which remain significant even at multivariate analysis (p = 0.0123 and p = 0.0010, respectively). Sensitivity analyses confirmed the robustness of causal estimates. Kaplan-Meier survival and Cox regression analyses further indicated that elevated LCN2 level, especially when combined with C-reactive protein levels, is an independent predictor of all-cause mortality and combined cerebral and cardiovascular event rates in CAD patients. Taken together, these results indicate that circulating LCN2 is largely a downstream marker of immune activation and impaired renal function. Elevated LCN2 levels independently predict poor long-term outcomes of CAD.

The accurate removal of intronic sequences from pre-mRNA by the spliceosome is essential for correct gene expression, with small nuclear RNAs (snRNAs) such as U4 playing structural and regulatory roles in catalyzing this. De novo variants in the highly constrained critical region including the T-loop region of RNU4-2 have been linked to ReNU syndrome, a neurodevelopmental disorder, but the broader mutational spectrum remains uncharacterized. Here, we show that, in a cohort of unresolved cases with neurodevelopmental disorder, monoallelic and biallelic RNU4-2 variants were identified in 16 affected individuals, expanding the genetic basis beyond the critical region: 12 with de novo T-loop variants and 4 from two families with compound heterozygous variants in non-critical regions (stem II, the k-turn, and the Sm-binding site). Previously reported functional mapping by saturation genome editing confirmed that most of the variant positions in this study are highly functionally constrained. Clinically, individuals with biallelic variants exhibited developmental delay and intellectual disability that were similar to but milder than those with monoallelic variants, notably lacking extracerebral organ involvement. These results suggest that pathogenic RNU4-2 variants act in both dominant and recessive manners, and that non-critical regions may also harbor disease-causing variants. More broadly, this study underscores the diagnostic importance of non-coding RNA genes in neurodevelopmental disorders and demonstrates the need to distinguish pathogenic variants from benign ones, together with their inheritance patterns.

Argyrophilic grain (AG) is a common neurodegenerative accumulation of 4 repeat tau in dendritic spine. Dementia with grain (DG) is defined as AGs with a sole pathological basis for cognitive decline. As with other multifactorial diseases, DG could result from interactions of environmental and genetic factors. However, the genetic basis of DG is largely unknown. To clarify the genetic architecture of DG pathogenesis, we conducted a genome-wide association study (GWAS) with 214 DG cases versus 12,405 controls. We have identified a candidate locus associated with the risk of DG, the SVIL locus on chromosome 10, with genome-wide significance (rs11595141, P = 4.86  $\times$  10^-8) in the GWAS. Transcriptome-wide association analysis using summary statistics for DG-GWAS identified DAPK2 (P_TWAS = 3.68  $\times$  10^-5) as a novel candidate causal gene for DG pathogenesis in the brain frontal cortex. The genetic association analysis for the APOE locus revealed that the APOE allele did not affect DG pathogenesis. We also identified new variants in the MAPT encoding tau protein that could potentially affect DG pathology. This is the first GWAS for DG, and our genetic findings provide biological and clinical insights into the pathogenesis of DG.

Transmembrane protein 53 (TMEM53) is an outer nuclear membrane protein that plays a crucial role in maintaining skeletal homeostasis. Pathogenic variants in TMEM53 have been identified as the genetic cause of craniotubular dysplasia, Ikegawa type (CTDI), a rare form of sclerosing bone dysplasia characterized by skull hyperostosis, cranial deformities, and increased bone density. To date, the causal association of bi-allelic pathogenic variants of TMEM53 in CTDI has been identified in 14 patients from eight unrelated families. Mechanistically, TMEM53 negatively regulates BMP-SMAD signaling by restricting the nuclear import of phosphorylated SMAD1/5/9, thereby modulating osteoblast differentiation and bone formation. This review summarizes the current understanding of TMEM53 function and the consequences of its deficiency. We aim to clarify genotype-phenotype correlations, outline therapeutic prospects for CTDI, and explore the distinct mechanisms underlying cranial and tubular bone formation.