Fanconi anemia (FA), a rare genetic disorder marked by bone marrow failure, congenital anomalies, and cancer predisposition, often presents diagnostic challenges due to phenotypic overlap with other conditions. While FANCAgene mutations account for the majority of FA cases, the complexity of its clinical presentation necessitates comprehensive molecular analysis. This study elucidates the intricate diagnostic pathway for FANCA-related FA within a Chinese family, while simultaneously establishing a critical hereditary differential diagnosis for ectrodactyly (split-hand/foot malformation). Through integrated genomic approaches—including whole-genome sequencing, copy number variation (CNV) analysis, and functional assays—the research uncovers a co-occurrence of pathogenic FANCAmutations and a novel EHMT1splice-site variant. The findings demonstrate that the proband's hematological manifestations stem from biallelic FANCAdefects, whereas the limb anomaly segregates independently with an EHMT1variant, highlighting the necessity of disentangling complex phenotypes for accurate genetic counseling and management.
The diagnostic odyssey began with a proband exhibiting classic signs of bone marrow failure, including pancytopenia and hypoplasia, initially suggestive of aplastic anemia. However, the presence of a family history involving paternal lineage members with ectrodactyly raised suspicion of a broader syndromic condition. Molecular investigation revealed a compound heterozygous state in the FANCAgene: a point mutation (c.154C>T) and a large genomic deletion (g.89865477_89895212del), the latter representing a novel pathogenic variant that enriches the known mutational spectrum. This biallelic disruption of FANCA, a core component of the FA DNA repair pathway, was functionally confirmed to cause partial protein deletion, directly explaining the proband's hematological deficits and cancer predisposition. This case underscores that FA should be a primary consideration in children with unexplained cytopenias, even in the absence of overt congenital malformations, and that CNV analysis is indispensable in genetic testing workflows, as standard sequencing may miss large deletions.
Intriguingly, the ectrodactyly phenotype observed in the paternal family members did not correlate with the FANCAmutations. Instead, pedigree analysis revealed complete segregation of the limb defect with a deep intronic variant in the EHMT1gene (c.2382+1750G>A). EHMT1haploinsufficiency is typically associated with Kleefstra syndrome, which features intellectual disability and distinctive facial features but rarely includes ectrodactyly. Functional characterization of this variant became paramount. Minigene splicing assays and RT-qPCR on patient blood samples demonstrated that the variant causes aberrant mRNA splicing and a significant reduction in EHMT1transcript levels. Western blot analysis further revealed a corresponding decrease in EHMT1 protein and its histone mark, H3K9me2, in heterozygous carriers. This compelling genotype-phenotype correlation, supported by reduced protein expression, provides strong evidence that this specific EHMT1variant is pathogenic and responsible for the limb anomaly, expanding the known phenotypic range of EHMT1-related disorders.
The study provides a masterclass in the differential diagnosis of complex genetic syndromes. It illustrates how a single family can harbor two distinct autosomal dominant and recessive conditions, which, when co-inherited, create a blended phenotype that mimics a single, highly penetrant syndrome. The proband inherited the EHMT1variant from the father but did not exhibit ectrodactyly, demonstrating variable expressivity. Crucially, the father, who carried both the EHMT1variant (causing his limb defect) and a heterozygous FANCAdeletion, was hematologically normal, as FA requires biallelic inactivation. This genetic dissection clarifies that the ectrodactyly is not a novel feature of FA but an independent trait, a distinction with profound implications for recurrence risk assessment. Genetic counseling for this family must now address two separate inheritance patterns: a 25% risk for FA and a 50% risk for the EHMT1-related limb anomaly in future offspring.
From a pathophysiological perspective, the findings illuminate two distinct molecular pathways. The FANCAdefect disrupts the FA/BRCA pathway, leading to genomic instability and hypersensitivity to DNA crosslinking agents. In contrast, the EHMT1variant impairs histone methyltransferase activity, disrupting epigenetic regulation of gene expression during embryonic development, particularly affecting limb morphogenesis. The reduced H3K9me2 levels observed in carriers suggest a mechanism of transcriptional dysregulation. This case adds to the growing evidence that intronic variants, even those deep within introns, can have severe clinical consequences by disrupting splicing regulation, emphasizing the need for whole-genome sequencing and functional validation in undiagnosed cases.
In conclusion, this research underscores the critical importance of a holistic genetic evaluation when faced with syndromic presentations. It advocates for a diagnostic strategy that moves beyond a single-gene hypothesis, employing broad genomic tools to dissect complex traits. The identification of the novel FANCAdeletion broadens the genetic landscape of FA, while the association of an EHMT1splice variant with ectrodactyly provides new insights into developmental biology. Ultimately, the study reinforces that precise molecular diagnosis is the cornerstone of personalized medicine, enabling accurate prognosis, targeted surveillance for FA-associated cancers, and informed reproductive choices for affected families.
DOI
10.1007/s11684-026-1202-6