Multilocus loss of DNA methylation in individuals with mutations in the histone H3 Lysine 4 Demethylase KDM5C

BMC Medical Genomics

Table 1 Top 13 CpG sites with loss of DNA methylation in KDM5C mutation cases with the lowest false discovery proportion level =0, the highest confidence level of 99.5% and delta beta ≤ −0.2

Target ID	KDM5C AVG Beta	Control AVG Beta	VUS AVG Beta	p-value	delta beta	delta Z	SYMBOL	DISTANCE TO TSS
cg02630888	0.41	0.89	0.91	9.98E-08	−0.48	2.03	FBXL5	−807
cg03387723	0.26	0.71	0.73	9.98E-08	−0.45	2.01	SCMH1	−676
cg16743289	0.24	0.52	0.53	9.98E-08	−0.28	2.02	CACYBP	−427
cg06736444	0.50	0.78	0.77	9.98E-08	−0.28	1.90	SRRM2	−861
cg22809047	0.31	0.59	0.54	9.98E-08	−0.27	1.91	RPL31	−490
cg19884658	0.55	0.77	0.74	9.98E-08	−0.23	1.98	KLHL21	−1,339
cg14719055	0.20	0.42	0.37	9.98E-08	−0.23	1.92	RBBP7	−1,218
cg16604218	0.09	0.31	0.35	9.98E-08	−0.22	1.84	EIF2B3	−349
cg20318748	0.07	0.29	0.18	9.98E-08	−0.22	1.95	NANP	−564
cg03621001	0.46	0.67	0.77	9.98E-08	−0.21	1.91	RAB8A	−771
cg00328227	0.08	0.28	0.30	9.98E-08	−0.2	1.95	C1orf59	−177
cg05072008	0.13	0.33	0.37	9.98E-08	−0.2	1.86	FIGNL1	−599
cg03221914	0.50	0.69	0.70	9.98E-08	−0.2	1.82	HIST1H2AJ	−813

VUS is p.R1546Q variant of unknown significance, AVG beta is mean beta value for each of three groups, delta beta is differences between mean of KDM5C mutations cases (N = 10) and controls (N = 19). Delta Z is delta beta divided by standard deviation of combined cases and controls data. All 13 CpG sites were located within CpG islands.