Whole-exome sequencing reveals the genetic landscape and polygenic susceptibility in 1241 patients with clinically suspected hemophagocytic lymphohistiocytosis

Expanding the Genomic Spectrum of NHLRC2-Associated FINCA Disease: Integrated Bioinformatic Characterization of a Novel Deep Intronic Variant Predicted to Activate a Pseudoexon

A male infant with a severe FINCA-like phenotype is reported, including early-onset hemolytic anemia, pulmonary involvement, neurodevelopmental impairment, growth failure, recurrent infections, and fatal progression at 8.5 months.

Targeted Analysis of Whole Exome Sequencing Data Identifies Biologically Plausible Causal Variants in Genetically Unresolved Oculocutaneous Albinism Patients From India

Background: Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder characterized by hypopigmentation and visual abnormalities. Despite eight established OCA-associated loci, some clinically diagnosed patients remain genetically unresolved, suggesting contributions from additional pigmentation-associated genes. Methods: Whole exome sequencing was performed in clinically diagnosed OCA patients lacking pathogenic variants or carrying a single heterozygous variant in known OCA genes (OCA1OCA8). Targeted analysis of 809 pigmentation-associated genes involved in melanogenesis, melanosomal transport, melanocyte differentiation, stem-cell maintenance, and pigmentation phenotypes was conducted. Variants were prioritized based on ACMG classification, rarity, predicted coding consequence, and biological relevance to pigmentation pathways. Results: In 5 patients with missing heritability, ACMG/Varsome/Ensembl Variant Effect Predictor-classified pathogenic/likely pathogenic rare variants were identified in pigmentation-associated genes including RAB38, MYO5A, and DOCK7, involved in melanosome biogenesis/maturation, transport, or pigmentation abnormalities. Potential disease-causing variants were also identified in BMPR1B, MYC, POLG, GNA11, and GGT1, which lack established roles in melanin biosynthesis or distribution but may contribute to pigmentation based on emerging evidence. Two patients harboured prioritised variants in multiple pigmentation-associated genes. Notably, 3 of 5 patients harboured previously identified changes in known OCA-causing genes in heterozygous condition, suggesting cumulative modifier or digenic/oligogenic contributions. Conclusions: Our findings broaden the spectrum of candidate pigmentation-associated variants in unresolved OCA cases and support possible oligogenic or modifier-driven mechanisms underlying phenotypic heterogeneity. However, these findings are hypothesis-generating and require functional validation.

Beyond in silico prediction: multi-omics to identify a pathogenic deep intronic HNRNPK variant in Au-Kline syndrome.

Whole-genome resequencing with multidimensional annotation revealed pathogenic networks in sirenomelia

The findings support a multilayered pathogenic model in which genetic variants collectively disrupt the core developmental pathways involved in posterior axis formation, vasculogenesis, and organogenesis and identify potential targets for future research and clinical applications.

A Novel Dominantly Segregating PSMB10 Splice-Site Variant in Familial Autoinflammatory Disease with Immunoproteasome and Interferon-Related Dysregulation

Background: Systemic autoinflammatory phenotypes can clinically overlap with Familial Mediterranean Fever and other monogenic autoinflammatory diseases, yet some cases remain unclassified in the absence of pathogenic variants in MEFV or other related genes. In this study, we aimed to investigate the genetic and molecular basis of an unclassified autoinflammatory phenotype in a two-generation family comprising four affected members and one unaffected member. Methods: We performed whole-exome sequencing in all family members and prioritized variants according to rarity, predicted functional impact, segregation pattern, and biological relevance to inflammatory pathways. Downstream molecular analyses were performed using PBMCs from affected individuals and the unaffected family member. Results: Whole-exome sequencing identified a novel splice-site variant in PSMB10 (NM_002801; c.56+1G>A) affecting the canonical splice donor site. The variant segregated with the autoinflammatory phenotype and was associated with reduced full-length PSMB10 transcript levels in patient-derived PBMCs, supporting a predicted loss-of-function effect. Although pathogenic variants in PSMB10 have previously been implicated in proteasome-associated autoinflammatory syndrome (PRAAS), the clinical presentation in this family differed from the classical PRAAS phenotype. Molecular analyses showed altered immunoproteasome-related gene expression and a severity-associated interferon-related response. Severely affected individuals showed increased expression of interferon-related genes, including ISG15, IFI35, and SIGLEC1, whereas mildly affected individuals showed lower or reduced expression patterns. Notably, the extent of these molecular alterations differed among family members and broadly reflected the observed clinical heterogeneity. Conclusions: We report a novel PSMB10 splice-site variant as a strong potential contributor to an unclassified autoinflammatory disease, with a predicted disruption of canonical splicing and loss of protein function. Our findings expand the clinical spectrum of immunoproteasome-associated disorders and suggest that immunoproteasome-related dysregulation and variable interferon responses may contribute to disease severity. The intrafamilial variability observed in this family suggests that additional genetic or immunogenetic factors may modify disease expression, even in autoinflammatory disorders that appear to follow a monogenic inheritance pattern.

Whole‐Exome Sequencing in Undiagnosed Muscular Dystrophies: A High Diagnostic Yield and Novel Insights From Iranian Families

Background Muscular dystrophies (MDs) are a genetically heterogeneous group of disorders, posing significant diagnostic challenges, especially in populations with high consanguinity. Despite advances in genetic testing, a substantial proportion of patients remain undiagnosed. Whole‐exome sequencing (WES) has emerged as a powerful tool for identifying causal variants in such unresolved cases. To identify the genetic basis of nondystrophinopathic MDs in Iranian families with inconclusive prior genetic testing and to evaluate the diagnostic yield and mutational spectrum in this population. Methods We performed WES on one affected individual from each of 10 unrelated Iranian families with clinically diagnosed MD. Candidate variants were prioritized based on in silico prediction tools (SIFT, PolyPhen‐2, CADD, SpliceAI), population frequency databases (gnomAD, 1000 Genomes, EVS), and ACMG/AMP guidelines. Findings were validated by Sanger sequencing, MLPA, and STR haplotype analysis. Segregation analysis was performed in available family members. Results WES led to a diagnostic yield of 69.2% (9/13 variants in 10 families) after segregation analysis and ACMG‐based reclassification. We identified 13 candidate variants in 10 known MD‐associated genes, including DYSF, SGCA, TK2, MAP3K20, LMNA, COL6A1, COL6A2, ITGA7, MICU1, and SGCB. Among these, seven variants (54%) were novel. The majority of cases (84.6%) followed an autosomal recessive pattern, consistent with high parental consanguinity (70%). Notably, a de novo splice‐site variant in COL6A2 (c.1053+1G>T) was identified in a sporadic case, confirming an autosomal dominant inheritance. Challenges in variant interpretation were observed in families with variants in tightly linked genes (COL6A1 and COL6A2), highlighting the role of linkage disequilibrium in founder populations. Conclusion WES is a highly effective diagnostic strategy for genetically heterogeneous MDs, particularly in consanguineous populations. Our study expands the mutational spectrum of MDs in Iran and provides critical data for genetic counseling, prenatal diagnosis, and future therapeutic development. The high rate of novel variants underscores the importance of population‐specific genomic studies.