Journal of Human Genetics最新文献

Thyroid hormones are central to regulating metabolism, growth, and development, yet their complex interactions with socioeconomic, metabolic, and genetic factors remain understudied in diverse populations. We compared thyroid profiles - free triiodothyronine (FT3), free thyroxine (FT4), and thyroid-stimulating hormone (TSH) in Indian adolescents with anthropometric traits, metabolic markers, and socioeconomic status (SES). We observed that adolescents from higher SES backgrounds exhibited greater metabolic dysregulation, altered thyroid profiles, and abnormalities in lipid and adipokine levels. Subclinical (16.1%) and clinical hypothyroidism (1.1%) were found to be prevalent in this population but were not associated with obesity. Instead, they showed links with dyslipidemia and altered adipokine profiles. To investigate the genetic basis of thyroid traits, we conducted an exome-wide association study (ExWAS, N = 4324), and a two-staged genome-wide association study (GWAS, N = 4854). The ExWAS revealed two novel loci for TSH (GYS2 and CEP162) and fifteen novel loci for FT4, including ZNF467, P3H3, CRLF3, SPATA2L, MEFV, THNSL2, COL27A1, COL28A1, IGSF3, ZNF732, MOG, GABBR1, HPF1, LOC440563, and SPEG. The GWAS identified novel associations at near-genome-wide significance for TSH (ACTL7B) and FT4 (LINC00648, YTHDC1, and C2CD4B). We also replicated established associations in FOXE1 and IGFBP5. Our findings suggest that SES, metabolic health, and genetics jointly influence thyroid function in Indian adolescents. The identification of population-specific loci emphasizes the importance of ancestry-informed genetic studies and supports the development of precision interventions to enhance pediatric thyroid health.

Tenascin-R (TNR) is an extracellular matrix glycoprotein that is essential for the formation of perineuronal nets in the central nervous system and is critical for neurite outgrowth, synaptic plasticity, and neural stem cell proliferation and differentiation. Biallelic TNR variants were reported to cause neurodevelopmental disorders with developmental delay, hypotonia, spasticity, and a variety of motor abnormalities. Here, we describe two Japanese siblings sharing novel compound heterozygous TNR missense variants (NM_003285.3:c.[1783 G > A];[3766 C > T] p.[(Asp595Asn)];[(Arg1256Cys)]) identified by exome and Sanger sequencing. The elder brother had dystonia, while the younger sister was asymptomatic except for adult-onset restless legs syndrome. Their development and intellect were normal. A total of 15 patients, including 13 previously reported patients, showed diverse phenotypic variability and severity, even among individuals sharing the same variants, indicating variable expressivity and reduced penetrance possibly influenced by genetic or environmental modifiers. Our findings extend the clinical spectrum of TNR-related disease and highlight the need for further accumulation of clinical cases and functional studies to understand genotype-phenotype correlations and the pathogenesis of diseases.

Whole-genome sequence information currently available for large-scale sequencing studies is biased toward European descent populations. Such bias causes difficulties in identifying disease-associated genetic variations in non-European populations, including the Japanese. Here, to comprehensively identify genetic variants, we sequenced 3135 individuals representing the genetic diversity of the Japanese population. Of the 44,757,785 identified variants, 31.0% exhibiting a minor allele frequency of <1% were novel. Using these variants, we constructed a reference haplotype and graph-structured reference sequence to facilitate accurate imputation and variant characterization. Our findings suggest that integrating genetic variations from ethnically diverse populations into the prevailing catalogs is essential to achieve precision medicine for all populations.

MECP2 duplication syndrome results from duplication of the MECP2 gene, encoding methyl-CpG-binding protein 2. Structural variations in this region can be detected by short-read next-generation sequencing, but resolving its precise genomic architecture remains challenging because of the involvement of complex and highly repetitive sequences. This study investigated the hidden structural variations using optical genome mapping and targeted long-read nanopore sequencing. We identified 14 breakpoints within the Xq28 regions encompassing MECP2 in four individuals from four families with MECP2 duplication syndrome. Combining the above methods enabled us to identify all the precise breakpoints, except for two inversions embedded within highly repetitive sequences. This also represents the most precise delineation to date of complex structural variants in MECP2 duplication syndrome. Notably, leveraging long nanopore reads (> 75 kb) allowed us to span low-copy repeat regions, including the approximately 72 kb J-group low-copy repeat which was difficult to be resolved, as well as GC-rich segments and dense clusters of short interspersed nuclear elements such as Alu, thus enhancing breakpoint-detection accuracy. We also detected previously underreported rare and complex rearrangement patterns. These findings highlight the power of integrating long-read sequencing with optical genome mapping for the delineation of complex genomic architectures, thus enhancing our understanding of the genomic structure underlying MECP2 duplication syndrome.

Congenital central hypoventilation syndrome (CCHS) is primarily caused by dominant PHOX2B mutations, with recessive LBX1 or MYO1H mutations being rare. Among PHOX2B mutations, polyalanine repeat expansion mutations (PARMs) are common, whereas non-PARMs (NPARMs) are less frequent. PHOX2B mutations are believed to act through loss-of-function mechanisms combined with dominant-negative and/or toxic gain-of-function effects. However, the role of PHOX2B haploinsufficiency remains unclear. We investigated the role of PHOX2B deletion and other genetic modifiers in CCHS. Among 93 patients without PHOX2B mutations, four were found to carry PHOX2B deletions via multiplex ligation-dependent probe amplification. Two had typical CCHS, whereas two siblings presented with mild sleep hypoventilation following CCHS symptoms in infancy. After ruling out pathogenic variants in LBX1 and MYO1H, we explored potential modifiers by analyzing sequence and methylation changes in the wild-type PHOX2B promoter and 3' untranslated region (3'UTR), and the coding regions of PHOX2A and MIR204. One female patient with CCHS carried a 3'UTR haplotype predicted to reduce PHOX2B expression via MIR204 interaction. To date, 15 informative cases with PHOX2B deletions (eight males, seven females) have been reported. Respiratory phenotypes included: CCHS (n = 5), CCHS with obstructive sleep apnea (OSA) (n = 1), OSA alone (n = 2), mild central sleep apnea (n = 1), mild central sleep hypoventilation or apnea following CCHS symptoms in infancy (n = 3), and asymptomatic (n = 3). These indicate that although a heterozygous PHOX2B deficiency alone is insufficient to cause CCHS, it may delay or impair the development of respiratory control.

Splice-disruptive variants represent an underrecognized yet critical category of disease-causing mutations. While canonical splice site disruptions have long been associated with genetic disorders, it is now increasingly evident that synonymous, deep-intronic, and regulatory variants can also perturb splicing events and contribute to diseases. As genomic diagnostics shift from phenotype-first to genome-first paradigms, there is an urgent need for systematic strategies to identify and interpret such variants-including those residing in noncoding regions that escape detection by traditional annotation pipelines. This review provides an integrative overview of current in silico approaches for the annotation and interpretation of splice-disruptive variants. We outline the mechanistic diversity of splicing aberrations and discuss recent advances in computational prediction frameworks, including both deep learning-based models and motif-oriented tools. In parallel, we summarize experimental strategies that are used to validate predicted splicing effects and assess their pathogenic relevance. Focusing on clinically relevant contexts, we discuss how splicing-aware variant interpretation enhances diagnostic yield, informs the reclassification of variants of uncertain significance, and uncovers targets for therapeutic intervention. Finally, we consider the implications of such interpretation for RNA-targeted strategies, including antisense oligonucleotides, small-molecule modulators, and emerging RNA-editing platforms, particularly in neuromuscular and other splicing-driven disorders. Together, these insights underscore the expanding role of in silico splicing prediction in precision medicine, offering new diagnostic and therapeutic avenues for rare and undiagnosed genetic diseases.

SEC24D is a key component of the Coat Protein Complex II, which plays a critical role in the selective sorting and transport of cargo proteins from the endoplasmic reticulum. This function is particularly essential for the secretion of extracellular matrix proteins, including collagens. Biallelic pathogenic variants in SEC24D have been associated with Cole-Carpenter Syndrome 2, a rare skeletal dysplasia characterized by craniofacial abnormalities and recurrent fractures. We reported a 12-year-old male patient presenting with recurrent bone fractures, severe skeletal deformities, limb shortening, craniofacial dysmorphism and pseudoarthrosis, a feature not previously reported in this condition. Whole-exome sequencing identified a novel homozygous synonymous variant in SEC24D (c.2361C>T; p.Asn787=), located 16 bases upstream of the donor splice site of intron 18. Functional analyses revealed markedly reduced SEC24D expression and aberrant exon 18 skipping, supported by RNA-seq, qPCR, and Western blot. This case provided the first functional evidence for a synonymous variant in SEC24D causing disease via splicing disruption and expands both the phenotypic and genotypic spectrum of Cole-Carpenter Syndrome 2.

Congenital myopathies are a group of genetically heterogeneous neuromuscular disorders characterized by early-onset hypotonia and muscle weakness. While many congenital myopathies have historically been attributed to structural defects in muscle fibers, accumulating evidence reveals that dysfunction of satellite cells-the resident stem cells essential for muscle growth and regeneration-can also cause congenital myopathy. In this review, we focus on four genes critical for satellite cell biology: PAX7, MYOD1, MEGF10, and MYMK, and discuss how pathogenic variants in these genes contribute to muscle pathology. Mutations in PAX7, a transcription factor essential for satellite cell specification and maintenance, have been identified in patients with progressive congenital myopathy and scoliosis. MYOD1 variants affect the transcriptional regulation of myogenic differentiation and have been reported in individuals with congenital muscle hypoplasia. Loss-of-function variants in MEGF10, which mediates satellite cell proliferation, result in early-onset myopathy characterized by severe weakness and areflexia. Mutations in MYMK, essential for myoblast fusion, lead to congenital myopathy with facial and axial weakness. Together, these studies illustrate that distinct steps in satellite cell function-including specification, commitment, proliferation, and fusion-are critical for normal muscle development and maintenance. Recognizing that genetic defects affecting any of these processes can lead to congenital myopathies, redefining the disease spectrum beyond purely structural muscle disorders. Expanding our understanding of satellite cell biology will be key to elucidating the full spectrum of congenital myopathies and identifying targeted therapeutic strategies.

Sudden unexpected death in epilepsy (SUDEP) is one of the most frequent causes of death in patients with epilepsy, though the pathogenesis of SUDEP has not been well elucidated. Here, we report novel heterozygous KCND3 variants, p.V401L and p.V401M, identified in young patients with refractory epilepsy (RE) and neurodevelopmental disorders, and the functional properties of these variants. We aimed to investigate the electrophysiological changes in de novo KCND3 variants and analyse the pharmacological effects of quinidine on these variants. Chinese hamster ovary (CHO) cells were transiently co-transfected with wild-type (WT) and/or variant KCND3 and Kcnip2. Transient outward potassium currents (I_to) were recorded using the whole-cell patch-clamp method. The inhibitory effect of quinidine on I_to was evaluated. In electrophysiological analysis, CHO cells expressing the variant channels showed a significant increase in current density compared with those expressing WT channels. The I_to activation curves were shifted significantly to the left, and significantly slower inactivation time constants were observed in both variant channels. Recovery from inactivation of the variant channels was significantly slower than that of WT. Quinidine suppressed I_to in a concentration-dependent manner and accelerated the slow inactivation of variant channels. In conclusion, de novo KCND3 variants identified in patients with RE and neurodevelopmental disorders showed gain and loss of function effects on I_to. These patients may be at risk of developing early repolarization syndrome, leading to SUDEP. Increased I_to was suppressed by quinidine, suggesting that it may be an effective therapy for RE and possibly for preventing SUDEP.