A77T V504M P480I E468GfsX2 R1481GfsX9 R1546Q Figure S1: Schematic diagram of the human KDM5C protein showing functional domains and positions of 5 mutations and p.R1546Q variant of unclear clinical significance. BRIGHT – DNA binding domain JmjC – Catalytic domain PHD – Plant Homeodomain

Figure S2: Scatter plots of DNA methylation determined by Illumina (X-axis) and pyrosequencing (Y-axis) at the same CpG site. Black diamonds are cases with KDM5C mutations, grey triangles are controls and light grey squares are individuals with p.R1546Q variant.

Figure S3: Visual mapping of all 31 data cases to the coordinate space defined by the first two principal components. The principal component analysis (PCA) was performed using all 23,837 CpG sites. The red dots represent the 10 mutation cases, the 19 light green dots represent controls, and the two dark green dots represent the benign mutation variants (R1546Q). The latter are the least separable from the mutation cases

Figure S4: Visual mapping of all 31 data cases to the coordinate space defined by the first two principal components. The principal component analysis (PCA) was performed using only the methylation levels at the 53 most significant CpG sites (the same ones as in Figure B). The red dots represent the 10 mutation cases, the 19 light green dots represent controls, and the two dark green dots represent the benign mutation variants (R1546Q). Although the PCA procedure did not use any information on the mutation status, the data distribution shows a clear separation between aberrant mutations on the one hand, and benign mutations and controls on the other hand.

Figure S5: Expression of FBXL5, SCMH1 and CACYBP in panel of human tissues. BT is brain total, FB- fetal brain, CC-cerebral cortex, CB-cerebellum, TL- temporal lobe, FL – frontal lobe, SC –spinal cord, K-kidney, H-heart, L-liver, SM-smooth muscle, SK-skeletal muscle, LCL-lymphoblastoid cell line. Error bars are standard deviation of duplicated q- PCR experiments.

*** * Figure S6: Disease association A) No association with ovarian cancer (GSE19711) C is control (N=274), OC – ovarian cancer (N=266). Sample highlighted by arrow exhibited loss of DNA methylation comparable to cases with KDM5C mutation. This could be due somatic mutation in KDM5C in this cancer patient or she could be a unaffected carrier of germline KDM5C mutation, B)Trisomy 21 study (GSE25395) disease association, C-is control (N=21), DS- is Down Syndrome caused by trisomy 21 (N=29). (FBXL5 median C=0.90, DS= 0.86, SCMH1 median C=0.75, DS= 0.77) NS A- ovarian cancer study B- trisomy 21 study