Comprehensive Assessment of the KDM2B-Associated Neurodevelopmental Disorder and the 12q24.31 Microdeletion Syndrome

The recently delineated KDM2B-associated neurodevelopmental disorder (NDD) is characterized by developmental delay and variable co-morbidity. Genotype-phenotype correlations are emerging, in particular a distinct clinical presentation caused by CxxC domain variants. We report here a novel intragenic deletion which leads to in vitro expression of a shortened KDM2B protein lacking the complete CxxC domain. In addition, we present data on 12 other individuals; two with larger 12q24.31 microdeletions, one with a frameshift variant, and nine with missense variants. We analyzed genotype-phenotype correlations of this cohort combined with previously reported individuals (n = 68) and classify 37 variants in 47 individuals as pathogenic or likely pathogenic. We observe a highly penetrant CxxC-related phenotype with distinct facial features supported by GestaltMatcher. In contrast, our findings point to variable expressivity and incomplete penetrance of loss-of-function variants and JmjC domain variants complicating variant classification and genetic counseling. We identify KDM2B as a strong contributor to the 12q24.31 microdeletion syndrome, while also addressing the role of additional genes in the region. Thus, our study defines the KDM2B-NDD's clinical spectrum and highlights the importance of integrating molecular, (epi)genetic, and phenotypic data in NDD diagnostics.