Okur-Chung neurodevelopmental syndrome (OCNDS; OMIM #617062) is an ultra-rare autosomal dominant disorder caused by heterozygous CSNK2A1 variants encoding CK2α; although the CSNK2A1 Foundation registry lists more than 350 diagnosed individuals worldwide, individual-level phenotypic data have been published for far fewer, and reports from Türkiye remain scarce. We retrospectively studied nine unrelated Turkish probands (4 F/5 M; 11 months to 23 years) from nine medical genetics centers across four geographic regions of Türkiye, diagnosed by exome sequencing (ES; n = 8) or chromosomal microarray (n = 1). A PRISMA 2020-compliant systematic review (inception-April 2026) provided an individual-level comparator pooled with our cohort (n = 61). Six distinct CSNK2A1 alterations were identified: the recurrent p.(Lys198Arg) p + 1 loop hotspot in 4/9 probands (44.4%); novel/rare p.(Arg195Gln) and p.(Asp156His) missense changes; two nonsense variants (p.(Tyr182Ter), p.(Arg333Ter)); and one ~537 kb heterozygous 20p13 contiguous deletion (arr[GRCh37] 20p13(61568_598427)x1). This proband also represents 20p13 deletion syndrome; previously reported cases of that entity were compared with our cohort. Core OCNDS features (developmental delay, intellectual disability, hypotonia, dysmorphism, behavioral disturbance) occurred at frequencies comparable to those in the pooled literature. Adult-onset obesity with type 2 diabetes (2/9) and hypogonadism (2/9), both essentially unreported in the predominantly pediatric pooled literature, were observed in two adolescent/young-adult males (one with p.(Lys198Arg), one with the 20p13 deletion). This series consolidates Lys198 as a recurrent hotspot across ethnically diverse cohorts, extends the structural-variant spectrum with the first Turkish CSNK2A1 contiguous-gene deletion, and supports adult-onset metabolic-reproductive complications as under-recognized OCNDS features. Systematic adolescent and adult metabolic-endocrine surveillance is recommended regardless of variant class.
Pathogenic variants in HNRNPK are associated with autosomal dominant Au-Kline syndrome (AKS, Au-Kline-Okamoto syndrome, OMIM #616580). This syndrome is characterized by developmental delay and intellectual disability, hypotonia, and distinctive facial features. Despite the use of whole-genome sequencing (WGS) as a powerful diagnostic tool, we nearly dismissed a novel intronic variant (NM_031263.4(HNRNPK):c.214-55 T > A) affecting HNRNPK splicing and function. Although commonly used bioinformatic splice prediction tools, including SpliceAI and PDIVAS, yielded inconclusive results, Face2Gene analysis indicated a high phenotypic similarity to AKS. Characteristic facial features described by Choufani et al. [1] supported the clinical diagnosis of AKS. Subsequent functional studies demonstrated aberrant splicing with intron retention, and DNA methylation profiling revealed a positive HNRNPK-specific episignature. These insights and the de novo status support an evaluation as likely pathogenic. This case report supports the relevance of facial analysis and comprehensive variant validation strategies, particularly for deep intronic variants with ambiguous in silico splicing predictions.
We report a 28-year-old infertile male presenting with markedly reduced progressive sperm motility and severe morphological abnormalities (normal morphology rate: 1%), accompanied by primary ciliary dyskinesia (PCD)-like symptoms, including chronic rhinitis, adolescent nasal polypectomy, and persistent rhinorrhea. Transmission electron microscopy (TEM) revealed ultrastructural defects involving the sperm head, nucleus, and flagellar axoneme. Whole-exome sequencing (WES) identified two novel compound heterozygous nonsense variants in the GAS8 gene: c.280 G > T (p.Glu94Ter) and c.382 C > T (p.Gln128Ter). Based on these findings, testicular sperm aspiration (TESA) combined with intracytoplasmic sperm injection (ICSI) was performed, resulting in a biochemical pregnancy. This case expands the mutational and phenotypic spectrum of GAS8 and provides additional clinical evidence relevant to genetic diagnosis, genetic counseling, and assisted reproductive management of male infertility accompanied by PCD-like symptoms.
Transposon-like human element (THE1) repeats are classified as part of the ERVL (endogenous retrovirus-like) -MaLR family and were previously thought to be remnants derived from retroviral infections in the germ cells of ancient primates. At present, at least 60,561 THE1 repeats have been mapped in the human genome, and they are divided into four subfamilies: THE1A, THE1B, THE1C, and THE1D. Although these repeats are largely silenced in somatic cells through multiple mechanisms, some of them are known to influence gene functions and genomic structures, particularly under disease conditions. Recently, we happened to identify the CIR1 driven from THE1B in the individuals with sarcoid myopathy (SM), which is characterized by the non-caseating granulomatous inflammation recognized in skeletal muscles biopsy. Retrotrans-genomics based on the COFFEE method showed that various THE1B fusion transcripts (THE1B/FTs) and retrotransposon-associated genomic dynamics in muscle of SM, including (1) splicing of THE1B to neighborhood exons, (2) expression of THE1B associated long noncoding RNAs in the intergenic regions, (3) ectopic expression of tissue specific transcripts driven by THE1B in SM, and (4) identification of a read through transcript, SIRPB1-SIRPD. Seven of eight THE1B/FTs downregulated by tofacitinib in cutaneous sarcoidosis were confined to the granuloma associated macrophage in sarcoidosis. The remaining transcript, SMFT4 exhibited stronger expression in mesenchymal stem cells. In addition, ectopic co-expression of canonical and LINE1 and THE1A-exonizing IL23R transcripts were identified in SM. This directory of THE1B/FTs in SM may serve as a fundamental molecular basis for understanding the pathogenesis of sarcoidosis.
Estimates of SNP-based heritability for atherosclerotic cardiovascular disease (ASCVD) vary widely across populations, complicating interpretation of genetic architecture. We compared SNP-based heritability and cross-cohort genetic correlation for ASCVD and its nested subphenotypes, coronary events (CE) and myocardial infarction (MI), across Geisinger’s MyCode, the UK Biobank, and the NIH’s All of Us using GWAS summary statistics and LD score regression. Heritability estimates differed significantly across cohorts, with consistently higher values in the UK Biobank and higher heritability for more narrowly defined phenotypes (MI) relative to broader ASCVD definitions. In contrast, genetic correlations between cohorts were uniformly high for all phenotypes, with confidence intervals spanning 1.0. These results suggest substantial sharing of common variant genetic effects across biobanks and indicate that cross-cohort differences in SNP-based heritability may primarily reflect differences in ASCVD ascertainment and phenotype capture rather than underlying genetic architecture.
Lung cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related mortality worldwide, with approximately 85% of cases classified as non-small cell lung cancer (NSCLC). Despite significant advances in diagnostic techniques and therapeutic strategies, including immunotherapy and targeted therapies, the prognosis of lung cancer remains poor, with an overall 5-year survival rate of approximately 22%. MicroRNAs (miRNAs) are small, single-stranded, non-coding RNA molecules that regulate gene expression at the post-transcriptional level and play critical roles in key biological processes, such as proliferation, apoptosis, migration, and invasion. miRNAs can function as oncogenes (oncomiRs) or tumor suppressors (TS-miRs), and their dysregulation is frequently observed in various malignancies, including NSCLC. Owing to their remarkable stability in serum and plasma, miRNAs have emerged as promising non-invasive biomarkers for the diagnosis and prognosis of NSCLC. In particular, exosomal miRNAs are encapsulated within a lipid bilayer that protects them from enzymatic degradation, thereby further enhancing their utility as liquid biopsy components and as potential biomarkers and therapeutic targets. Moreover, a single miRNA can regulate multiple target genes, highlighting their promise as therapeutic targets. This review summarizes the diagnostic, prognostic, predictive, and therapeutic potential of tissue-derived, circulating, and exosomal miRNAs in NSCLC and discusses the major challenges limiting the clinical translation of miRNA-based biomarkers and therapeutics.
Peroxiredoxin 3 (PRDX3) encodes a mitochondrially localized antioxidant enzyme. Biallelic pathogenic variants in PRDX3 cause autosomal recessive spinocerebellar ataxia type 32 (SCAR32), a rare form of spinocerebellar ataxia. We report four unrelated Japanese patients with SCAR32 identified among 411 ataxia cases negative for repeat expansion disorders. Age at onset was 9-30 years, with a predominantly pure cerebellar phenotype; one patient had autoimmune comorbidities. MRI showed cerebellar atrophy and T2 hyperintensity in dentate nuclei in all patients, and three had cerebellar cortical T2 hyperintensity, a potentially representative feature of SCAR32. Genetic analysis identified one homozygous and three compound heterozygous PRDX3 nonsense variants: the previously reported p.Arg207* in all patients, p.Arg170* in two, and novel p.Gln50* in one. The relatively high p.Arg207* allele frequency in East Asians and the 0.97% prevalence in our undiagnosed ataxia cohort support SCAR32 as an important cause of early-onset autosomal recessive cerebellar ataxia in Japan.
Biallelic SLC20A2 variants have recently been linked to a severe childhood-onset phenotype distinct from classical adult-onset primary brain calcification, but the molecular and radiologic consequences of homozygous truncating variants remain incompletely defined. We describe a child with severe early-onset neurodevelopmental disease caused by a homozygous SLC20A2 nonsense variant and provide clinical, neuroradiologic, segregation, and transcript-level characterization. The patient presented in early infancy with refractory seizures, severe hypotonia, left hemiplegia, profound developmental impairment, bilateral cataracts, and progressive intracranial calcification. Neuroimaging showed an unusual vascular and leptomeningeal calcification pattern with arterial narrowing, cytotoxic edema, subdural effusion, and rapid cerebral atrophy. Whole-exome sequencing identified a homozygous truncating variant, NM_001257180.2:c.1652 G > A, p.(Trp551Ter), in SLC20A2; both parents were heterozygous and showed radiologic findings consistent with SLC20A2-related primary brain calcification. RNA sequencing and RT-qPCR demonstrated marked reduction of SLC20A2 expression in patient-derived fibroblasts, supporting biallelic loss of function, whereas XPR1 expression was not significantly altered. Patient fibroblasts did not show overt Golgi fragmentation or ciliogenesis defects. These findings support a dose-dependent SLC20A2 disease spectrum and expand the phenotype associated with biallelic loss of function from primary brain calcification toward severe early-onset neurodevelopmental disorder with prominent vascular and leptomeningeal calcification.
Mucopolysaccharidosis IVA (MPS IVA) is a lysosomal storage disorder caused by a deficiency of N-acetylgalactosamine-6-sulfate sulfatase (GALNS), leading to progressive accumulation of keratan sulfate (KS) and chondroitin-6-sulfate (C6S) and resulting in systemic skeletal dysplasia. Severe, early-onset disease is frequently associated with destabilizing structural missense variants, including p.R386C. To model a loss-of-function missense variant associated with severe MPS IVA, we generated a GalnsR384C knock-in mouse, the murine ortholog of the most common human variant, p.R386C. Biochemical, histological, and skeletal phenotypes were evaluated across multiple tissues, and bone microarchitecture was assessed using microcomputed tomography (micro-CT). Genomic and biochemical assays were performed to assess allelic integrity, and principal component analysis (PCA) was used to integrate biochemical and structural parameters. GalnsR384C mice exhibited significantly reduced GALNS activity and elevated KS levels across various tissues. Histological examination revealed considerable vacuolization in cartilage and cardiac valves, while micro-CT illustrated altered bone microarchitecture consistent with disrupted endochondral ossification. During allele validation, a secondary missense variant (p.R384Y) was identified and characterized as a comparative model that led to defective GALNS activity, substrate accumulation, and analogous skeletal and cardiovascular pathology. PCA demonstrated clear differentiation between WT and mutant groups, with considerable multivariate overlap observed between GalnsR384C and GalnsR384Y mice. In conclusion, GalnsR384C and GalnsR384Y mice recapitulate key biochemical, skeletal, and histopathological features of MPS IVA and provide well-characterized murine models of severe GALNS loss-of-function resulting from clinically relevant missense variants. Rigorous genomic validation underscores the importance of careful allele-level characterization during genome-editing-based model generation.
Cell-free fetal mRNA (cff-mRNA) in amniotic fluid has emerged as a valuable source of molecular information reflecting fetal development. We aimed to identify cff-mRNA transcripts showing gestational-age-dependent expression patterns in human amniotic fluid and to characterize their expression changes across gestation. Cell-free mRNAs from amniotic fluid samples at 16 and 38 weeks' gestation (n = 1 each) were analyzed by RNA sequencing. Candidate mRNAs showing gestational-age-dependent transcriptional changes were selected based on an expression level of ≥300 transcripts per million (TPM) at either 16 or 38 weeks' gestation and a 38-week/16-week expression ratio of ≥20. As confirmation analysis, RT-qPCR was performed using independent amniotic fluid samples collected at 16 weeks' gestation (n = 20) and 38 weeks' gestation (n = 20). Overall, 1587 mRNAs were identified by RNA sequencing analysis. Among mRNAs showing gestational-age-dependent increases in expression, six candidate genes (SFTPC, NAA10, CALML5, SMIM29, IFITM3P6, and ARF-1) were selected for RT-qPCR validation based on expression changes and tissue representation. RT-qPCR confirmed that all six genes were significantly more highly expressed at 38 weeks than at 16 weeks (all p < 0.0001; Mann-Whitney U test). This study identified candidate cff-mRNAs in human amniotic fluid that exhibit gestational-age-dependent expression patterns. These findings provide preliminary insights into developmental transcriptional changes during fetal development and contribute to our understanding of the amniotic fluid transcriptome. Further validation of the findings obtained here in larger, independent cohorts is required.
Non-invasive prenatal testing (NIPT) generates vast amounts of low-depth sequencing data, offering a valuable resource for studying maternal genetic traits. However, standard NIPT genotype imputation workflows include time-consuming post-alignment processing steps from GATK, whose benefits for low-depth data remain uncertain. Additionally, merging imputation results from large, batch-processed cohorts presents a challenge, particularly for accurately combining imputation information scores (INFO). This study therefore aimed to develop an efficient imputation pipeline for NIPT data by evaluating the necessity of standard post-alignment steps and validating a batch-merging strategy, using maternal folate metabolism genotyping as a clinical application. The omission of GATK post-alignment steps, including duplicate marking and base quality score recalibration, did not compromise imputation accuracy across multiple simulated low depths but substantially reduced computational time. A sample-size weighted averaging method enabled accurate merging of imputation INFO scores from batch-processed data, yielding results nearly identical to single-cohort imputation for high-quality variants. Applying this optimized pipeline to 517 real-world NIPT samples demonstrated high genotype and allele concordance for the MTHFR rs1801131 and MTRR rs1801394 loci when compared to a sequencing capture method, with both metrics exceeding 96% at GP80. In conclusion, this study validates a simplified, computationally efficient imputation workflow for low-depth NIPT data. It enables accurate assessment of maternal folate metabolism genotypes, offering a cost-effective strategy for large-scale genetic screening of specific maternal traits without additional experimental burden, using existing clinical sequencing data.
Skeletal muscle excitation-contraction coupling (ECC) is a highly specialized process that converts membrane depolarization into contraction through tightly regulated intracellular Ca²⁺ dynamics. Recent advances in molecular genetics have expanded the spectrum of skeletal muscle disorders associated with ECC-related proteins, including congenital myopathies, malignant hyperthermia susceptibility, exertional rhabdomyolysis, exertional heat illness, and related episodic disorders. Although these disorders have traditionally been classified according to clinical manifestations, pathological findings, and causative genes, accumulating evidence suggests that genetically and clinically heterogeneous disorders converge on overlapping abnormalities in intracellular Ca²⁺ handling and ECC function. This review provides an integrative overview of ECC-related skeletal muscle disorders from the perspective of shared abnormalities in intracellular Ca²⁺ handling and the molecular mechanisms that underlie them. We discuss how pathogenic variants affecting the voltage-sensing skeletal muscle L-type calcium channel (CaV1.1), the ryanodine receptor type 1 (RyR1), and other triad-associated proteins disrupt Ca²⁺ release from the sarcoplasmic reticulum (SR), luminal Ca²⁺ regulation, and SR Ca²⁺ reuptake, leading to diverse but partially convergent phenotypes. We also discuss secondary pathological changes associated with chronic intracellular Ca²⁺ dysregulation, including mitochondrial dysfunction, oxidative stress, and skeletal muscle remodeling. Finally, we present a functional perspective centered on intracellular Ca²⁺ handling that complements conventional genetic and clinicopathological classifications of ECC-related skeletal muscle disorders.
Congenital disorders of glycosylation (CDG) comprise a diverse group of inherited metabolic diseases caused by defects in glycan biosynthesis. SSR4-CDG is an ultra-rare X-linked disorder caused by pathogenic variants in SSR4, which encodes a subunit of the translocon-associated protein (TRAP) complex involved in endoplasmic reticulum N-linked glycosylation. To date, only a limited number of patients have been reported, and all previously reported pathogenic variants have been truncating or splice-altering variants. Here, we report two unrelated patients with SSR4-CDG identified by trio-based whole-exome sequencing. Patient 1 carried a de novo nonsense variant and presented with severe intellectual disability and autism spectrum disorder. Notably, he is currently alive at age 56, providing insight into the long-term clinical course of this condition. Patient 2 harbored a maternally inherited in-frame insertion-deletion variant that was initially classified as a variant of uncertain significance. He showed severe developmental delay, failure to thrive, epilepsy, and hyperkinetic movements. Repeat glycan analysis revealed a CDG type I pattern, transcript analysis demonstrated aberrant transcripts with an expanded deletion, and structural modeling suggested destabilization of the β-barrel domain of SSR4, together supporting reclassification as likely pathogenic. These findings expand the clinical and molecular spectrum of SSR4-CDG, including survival into adulthood and diverse neurological manifestations. Our study also illustrates the challenges in interpreting variants associated with subtle biochemical abnormalities and underscores the importance of integrating biochemical, genetic, transcript, and modeling-based structural assessment for accurate diagnosis of rare CDG subtypes.
Non-obstructive azoospermia (NOA) represents the most severe type of male infertility. The linker of nucleoskeleton and cytoskeleton (LINC) complex and the TERB1-TERB2-MAJIN (TTM) telomere-tethering complex are essential for meiotic chromosome dynamics; however, pathogenic variants in these pathways have rarely been characterized in human NOA. In this study, whole-exome sequencing (WES) identified novel bi-allelic variants in genes encoding components of the LINC and TTM complexes in patients with NOA, including compound heterozygous variants in KASH5 (NM_144688.5:c.149-1G>A; NM_144688.5:c.876+1G>A), homozygous variant in TERB1 (NM_001136505:c.1814G>A, p.Arg605Gln), compound heterozygous variants in TERB2 (NM_152448.3:c.39dup, p.Ser14Ter; NM_152448.3:c.522A>G, p.Thr174Thr), and homozygous splice-site variant in MAJIN (NM_001318808.2:c.219+1G>T). Testicular histology and immunofluorescence analyses concordantly demonstrated a shared phenotype of meiotic prophase I arrest and absence of post-meiotic germ cells in these patients. Minigene assays demonstrated that the splice-site variants in KASH5 (c.149-1G>A; c.876+1G>A), TERB2 (c.522A>G), and MAJIN (c.219+1G>T) induced aberrant exon-skipping events. The frameshift variant in TERB2 (c.39dup) resulted in complete loss of protein expression, whereas the missense variant of TERB1 (c.1814G>A) led to markedly reduced protein levels and disruption of the TRF1-binding domain via in silico structural modeling. Collectively, this study demonstrated that novel variants in LINC and TTM complexes of meiotic chromosome dynamics are associated with meiotic arrest and NOA, which expanded the mutational spectrum of LINC- and TTM-related genes and deepen our knowledge of the role of LINC- and TTM-complex in male fertility.
Hereditary breast and ovarian cancer (HBOC) syndrome, caused by pathogenic variants in BRCA1 or BRCA2, is associated with increased risks of breast, ovarian, pancreatic, and prostate cancers. Although long-term, multi-organ surveillance is recommended, real-world data on its implementation in Japan remain limited. We conducted a web-based cross-sectional survey among 274 individuals registered for a hybrid public lecture at Keio University Hospital in 2024; 121 responded (44.2%). Respondents included HBOC carriers, healthcare professionals, and the general public. Among 66 carriers, 57 were affected and 9 were unaffected. Although the sample size is small, surveillance uptake was high among affected carriers (89.5%). Approximately half of affected carriers undergoing surveillance reported satisfaction, while nearly half underwent surveillance at multiple institutions, suggesting fragmented care. Across all groups including healthcare professionals and the general public, the most acceptable annual cost was less than 50,000 yen. Healthcare professionals identified interdepartmental coordination and shortages of genetic specialists as major challenges. These exploratory findings suggest that affordability, convenience, interdepartmental and interfacility coordination, and the availability of genetic medicine professionals may be important considerations in efforts to develop sustainable HBOC surveillance systems in Japan.
Normal-tension glaucoma (NTG) is an age-related cause of irreversible vision loss, yet the contribution of genetic variants to susceptibility across the lifespan remains unclear. The splice-site variant METTL23 c.84+60delAT (delAT), which induces aberrant exon skipping, has been implicated in NTG. We evaluated the age-dependent genetic risk associated with delAT by integrating age-stratified carrier frequency analyses in population datasets with age-specific case control association analyses in 3843 individuals. In the gnomAD database, the frequency of delAT carriers declined sharply with age, decreasing approximately sixfold in individuals aged ≥40 years. Consistent with this finding, case-control analyses demonstrated increasing effect sizes with advancing age, with odds ratios of 1.84 in individuals aged ≥40 years and 2.59 in those ≥50 years (P = 0.039). These complementary analyses provide convergent evidence that delAT confers an age-dependent increase in NTG risk, underscoring the importance of incorporating age into genetic analyses of late-onset disease.
Spinocerebellar ataxia type 36 (SCA36)-caused by a GGCCTG hexanucleotide repeat expansion in the NOP56 gene-has traditionally been considered to originate from a founder effect in the Ashida River basin of southern Japan. However, its genetic background remains incompletely understood. In this study, we analyzed five Japanese patients with SCA36 from four unrelated families using long-read sequencing to determine repeat length and reconstruct detailed haplotypes around the NOP56 locus. We successfully resolved extended haplotypes ranging from approximately 90 kb to 1.3 Mb. All five individuals shared a 5.3-kb haplotype adjacent to the repeat expansion, while four patients from northern Japan shared a larger haplotype block of at least 95.2 kb. Comparison with seven previously reported Korean SCA36 cases revealed a shared 4.2-kb haplotype, and available data from other populations were concordant within a ~ 2.1-kb core region. Notably, the shared 5.3-kb haplotype is relatively common in the general population, suggesting that the underlying core haplotype may represent a permissive haplotypic background rather than a unique founder haplotype. These findings indicate that SCA36 is unlikely to be explained solely by a regional founder in southern Japan. Instead, a shared permissive haplotypic background may underlie repeat expansion, with large pathogenic expansion arising independently in different populations. This pattern may be consistent with a stepwise process of repeat expansion.
Biallelic pathogenic variants in the MYPN gene are a known cause of congenital myopathy, and exonic variants that activate cryptic splice sites have not been previously reported. Here, we report a Chinese proband with congenital myopathy carrying a homozygous nonsense variant, c.2986C>T (p.Arg996Ter), in exon 14 of the MYPN gene. Transcriptional analysis suggested that this variant likely activated a cryptic donor splice site, truncating the last 91 nucleotides of exon 14 during pre-mRNA splicing. Western blotting and immunofluorescence confirmed a deficiency of myopalladin protein in the proband’s skeletal muscle. Our study highlights that exonic variants, particularly those distant from exon-intron junctions, can induce aberrant pre-mRNA splicing. This insight is crucial for interpreting the pathogenicity of variants of uncertain significance and enhancing diagnostic yield in genetic testing.
