Clinical and Molecular Spectrum of KBG Syndrome in the Largest Independent Turkish Cohort: Novel ANKRD11 Variants, 16q24.3 Deletions, and Structural Insights for Robust ANKRD11 Variant Interpretation.

Abstract

Background KBG syndrome (OMIM #148050) is a rare autosomal dominant disorder caused by haploinsufficiency of ANKRD11 on chromosome 16q24.3. It is characterized by distinctive craniofacial features, macrodontia, short stature, skeletal anomalies, and neurodevelopmental impairment. Populations outside Western Europe and North America remain underrepresented in the literature, and cohorts that comprehensively evaluate both sequence variants and copy-number variants (CNVs) remain limited. Aims To characterize the clinical and molecular spectrum of KBG syndrome associated with an identified ANKRD11 alteration in a Turkish multicenter cohort, investigate genotype-phenotype correlations, and assess the contributions of sequence variants and CNVs to disease diagnosis and variant interpretation. Study Design Multicenter, retrospective cohort study. Methods We retrospectively evaluated the clinical, anthropometric, and molecular characteristics of 36 Turkish individuals with KBG syndrome and an identified ANKRD11 alteration (31 pathogenic or likely pathogenic variants and five variants of uncertain significance) who were recruited from multiple pediatric genetics centers. Molecular analyses included whole-exome sequencing, clinical exome sequencing, and chromosomal microarray analysis (CMA). Variants were classified according to the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines. An exploratory genotype-phenotype analysis was performed by comparing truncating, non-truncating sequence variant, and CNV/deletion groups using Fisher's exact and Mann-Whitney U tests, with Benjamini-Hochberg correction for multiple comparisons. Results The cohort comprised 22 males and 14 females (male-to-female ratio, 1.57:1). A total of 29 distinct ANKRD11 alterations were identified, including 25 sequence variants and four distinct 16q24.3 deletions. Truncating variants were predominant (n = 25), while 11 sequence variants and four distinct 16q24.3 deletions further expanded the known molecular spectrum of KBG syndrome. The recurrent variant c.1903_1907del (p.Lys635GlnfsTer26) was identified in three unrelated individuals, supporting exon 9 as a major mutational hotspot. All three missense variants were clustered within the C-terminal degron, consistent with the previously reported enrichment of pathogenic missense variants in this functionally important region. 16q24.3 deletions accounted for 19.4% (7/36) of cases, underscoring the diagnostic value of copy-number analysis in patients with suspected KBG syndrome. Conclusion This study represents the largest independent Turkish multicenter cohort of individuals with KBG syndrome reported to date. Our findings expand the clinical and molecular spectrum associated with ANKRD11, provide further evidence supporting haploinsufficiency as the primary disease mechanism, and underscore the diagnostic importance of CMA in syndromic neurodevelopmental disorders. Furthermore, integrating our cohort data with published findings provides a practical framework for interpreting ANKRD11 variants, particularly those involving the 5' regulatory region and C-terminal missense variants.