A Case Report on the Rare C.-35G>C F9 Variant and Genotype—Phenotype Analysis in Hemophilia B Leyden

Hemophilia B Leyden (HBL) is a rare and clinically distinctive subtype of hemophilia B, accounting for approximately 1 to 3% of cases, characterized by low factor IX (FIX) activity in childhood with spontaneous phenotypic improvement after puberty.[ 1 ] [ 2 ] This unique phenotype was first described in Dutch families in 1970, where affected males exhibited severe bleeding symptoms early in life but showed gradual normalization of FIX levels during adolescence.[ 3 ] While the original description involved a severe phenotype, subsequent reports have shown that HBL may also present with moderate or mild hemophilia B in childhood, with the same characteristic pattern of FIX increase over time.[ 4 ] Unlike classical hemophilia B, which is caused mostly by coding-region mutations that result in a consistent lifelong deficiency, HBL is distinguished by promoter variants that disrupt developmental transcriptional regulation and lead to a time-dependent natural history characterized by spontaneous FIX improvement with age.[ 5 ] [ 6 ] Improvement was traditionally attributed to the rising androgen levels that activate alternative transcriptional pathways through the androgen receptor (AR).[ 7 ] [ 8 ] However, this androgen-centered model has been increasingly questioned: A substantial proportion of children show FIX improvement before the onset of puberty, independent of androgen exposure,[ 4 ] [ 9 ] and transgenic animal models have demonstrated a growth hormone-mediated, and age-related mechanism that operates independently of sex.[ 10 ] The F9 promoter contains binding sites for several transcription factors, including hepatocyte nuclear factor 4-α (HNF4α), CCAAT/enhancer-binding protein α (C/EBPα), and ONECUT1/2 that coordinate developmental regulation of F9 expression,[ 11 ] [ 12 ] [ 13 ] although recent evidence suggests these mechanisms are more complex and variant-specific[ 4 ] ([ Fig. 1 ]). Fig. 1 Schematic representation of the human F9 promoter region and known variants associated with hemophilia B Leyden (HBL). The promoter is shown linearly relative to the transcription start site (TSS, +1; black arrow indicates the direction of transcription) and the start of exon 1. Colored boxes denote approximate transcription factor-binding regions characterized in previous functional studies: the androgen-responsive element (ARE, −65 to −51), the ONECUT/HNF6-binding region (≈ −35), the HNF4α-binding region (≈ −26 to −17), and the C/EBPα-binding region (≈ −6 to −5). The horizontal bracket denotes the previously described “Leyden-specific region” (c.-50 to c.-18), within which promoter variants characteristically produce the partial, often puberty-associated, normalization of factor IX levels that defines the HBL phenotype. A more distal regulatory element (Ets/GABP-binding site) is indicated to the left of a scale-break (indicated by “NN”); functional evidence for this element exists, but its precise nucleotide position has not been mapped, and this segment is, therefore, not drawn to scale. Circles indicate the position of each known promoter variant and are color-coded according to reported clinical significance: red, pathogenic; orange, likely pathogenic. The variant identified in the present case, c.-35G > C, is marked with a star (★) shown in bold and depicted in gray to indicate an HBL-associated promoter variant that currently lacks a formal ACMG/AMP pathogenic or likely pathogenic classification. As c.-35G > A and c.-35G > C affect the same nucleotide position, they are shown stacked vertically at −35 for clarity. Because c.-22delT, c.-20T > C/T > A, c.-19C > G and c.-17A > G/A > C cluster within a 5-bp interval of the HNF4α-binding region, they are grouped in a callout box connected to their respective positions by a leader line. Solid vertical lines connect each variant circle to its corresponding position on the promoter axis. ACMG/AMP, American College of Medical Genetics and Genomics/Association for Molecular Pathology; bp, base pairs; C/EBPα, CCAAT/enhancer-binding protein α; Ets/GABP, E-twenty-six/GA-binding protein; HNF4α, hepatocyte nuclear factor 4-α; ONECUT, one cut homeobox (also known as HNF6). The International Pediatric Network of Hemophilia Management Registry (PedNet) data show that the common c.-35G > A variant improves earlier and more consistently than other non-c.-35G > A variants, including c.-35G > C.[ 4 ] We report a patient with HBL caused by the rare c.-35G > C promoter variant. Publication History Received: 21 April 2026 Accepted after revision: 27 July 2026 Article published online: 11 August 2026 © 2026. Thieme. All rights reserved. Thieme Medical Publishers, Inc. 333 Seventh Avenue, 18th Floor, New York, NY 10001, USA