Next generation sequencing is widely used to link genetic variants to diseases, and it has massively accelerated the diagnosis and characterization of rare genetic diseases. After initial bioinformatic data processing, the interactive analysis of genome, exome, and panel sequencing data typically starts from lists of genetic variants in VCF format. Medical geneticists filter and annotate these lists to identify variants that may be relevant for the disease under investigation, or to select variants that are reported in a clinical diagnostics setting. We developed VCF.Filter to facilitate the search for disease-linked variants, providing a standalone Java program with a user-friendly interface for interactive variant filtering and annotation. VCF.Filter allows the user to define a broad range of filtering criteria through a graphical interface. Common workflows such as trio analysis and cohort-based filtering are pre-configured, and more complex analyses can be performed using VCF.Filter's support for custom annotations and filtering criteria. All filtering is documented in the results file, thus providing traceability of the interactive variant prioritization. VCF.Filter is an open source tool that is freely and openly available at http://vcffilter.rarediseases.at.

IKAROS is a transcription factor forming homo/hetero-dimers and regulating lymphocyte development and function. Germline mutations affecting IKAROS N-terminal DNA binding domain, acting in a haploinsufficient or dominant negative manner, cause immunodeficiency. Herein we describe four germline heterozygous IKAROS variants affecting its C-terminal dimerization domain by haploinsufficiency, in four unrelated families. Index patients presented with hematologic disease consisting of cytopenias (thrombocytopenia, anemia, neutropenia)/Evans syndrome, and malignancies (T-ALL, Burkitt lymphoma). These mutations are partially or completely deficient to form homo- and hetero-dimers, but do not affect the wild type allele function. Moreover, they alter key mechanisms of IKAROS gene regulation including sumoylation, protein stability, and the recruitment of the nucleosome remodeling and deacetylase complex; none of them affected the N-terminal DNA binding. These C-terminal dimerization mutations are largely associated with hematologic disorders, display dimerization haploinsufficency, incomplete clinical penetrance, and differ from previously reported allelic variants in their mechanism of action. Dimerization mutants contribute to the growing spectrum of IKAROS-associated diseases displaying a genotype-phenotype correlation.