However, fourteen rare pathogenic variants were found only in chordoma cases and were absent from all 598 controls (variants in these genes: AKT1, ATP6V1B2, DEPTOR, FOXA2, HHIP, NFE2L2, PAX6, PDK1, PRKACA, PTCH1, SMARCB1, SOX21, SOX9 and TBXT). This evidence concerns the gene FOXA2 and chordoma.