Table 1.

Sample list and variants.

Sample	Patient sex	Patient age (years)	Batch	Used for	Predicted pathogenicity	Sample type	TET3 variant(s)
1a	Female	3	1	Signature discovery	Pathogenic	TET3 (BA)	c.3215T>G (p.Phe1072Cys)c; c.3226G>A (p.Ala1076Thr)c
2a	Male	21	1	Signature discovery	Pathogenic	TET3 (BA)	c.2722G>T (p.Val908Leu); c.2722G>T (p.Val908Leu)c
3a	Female	27	1	Signature discovery	Pathogenic	TET3 (BA)	c.2722G>T (p.Val908Leu); c.2722G>T (p.Val908Leu)c
4a	Male	5	1	Signature discovery	Pathogenic	TET3 (MA)	c.4977_4983del (p.His1660Profs*52)
5a	Male	57	1	Signature discovery	Pathogenic	TET3 (MA)	c.4977_4983del (p.His1660Profs*52)
6a	Female	11	1	Signature discovery	Pathogenic	TET3 (MAb)	c.3265G>A (p.Val1089Met)c; c.2254C>T (p.Arg752Cys)c
7	Female	10	1	Signature validation	NA	Family member controld	Familial variant absent by Sanger sequencing
8	Male	23	1	Signature validation	NA	Family member controle	Familial variant absent by Sanger sequencing
9	Female	44	1	Signature validation	NA	Family member controlf	Familial variant absent by exome sequencing
10	Female	10	1	Signature validation	NA	Family member controlg	Familial variants absent by Sanger, exome sequencing
11	Male	50	1	Signature validation	Benign	TET3 (MA)	c.2254C>T (p.Arg752Cys)c
12a	Male	6	2	Signature validation	Pathogenic	TET3 (MA)	c.5083C>T (p.Gln1695*)
13a	Male	5	2	Signature validation	Pathogenic	TET3 (MA)	c.3100C>T (p.Arg1034*)
14a	Female	46	1	Signature validation	Pathogenic	TET3 (MA)	c.3265G>A (p.Val1089Met)c
15a	Male	64	1	Signature validation	Pathogenic	TET3 (MA)	c.2722G>T (p.Val908Leu)c
16a	Female	28	1	Signature validation	Pathogenic	TET3 (MA)	c.3226G>A (p.Ala1076Thr)c
17	Female	2	2	Testing	Unknown	TET3 VUS (BA)	c.1483C>T (p.Pro495Ser); c.3883G>A (p.Val1295Ile)
18	Female	11	1	Testing	Unknown	TET3 VUS (BA)	c.4513G>A (p.Gly1505Arg); c. 5237G>C (p.Trp1746Ser)
19	Female	27	2	Testing	Unknown	TET3 VUS (MA)	c.1483C>T (p.Pro495Ser)
20	Male	46	2	Testing	Unknown	TET3 VUS (MA)	c.3883G>A (p.Val1295Ile)
21a	Male	21	2	Testing	Unknown	TET3 VUS (MA)	c.2732G>A (p.Arg911Gln)
22a	Male	9	4	Testing	Unknown	TET3 VUS (MA)	c.5048G>A p.(Arg1683His)
23	Female	42	1	Testing	Unknown	TET3 VUS (MA)	c.4513G>A (p.Gly1505Arg)
24	Male	47	1	Testing	Unknown	TET3 VUS (MA)	c.5237G>C (p.Trp1746Ser)
25a	Female	54	1	Testing	Unknown	TET3 VUS (MA)	c.2036dupC (p.Thr680Tyrfs*26)h
26a	Male	6	1	Testing	Unknown	TET3 VUS (MA)	c.2036dupC (p.Thr680Tyrfs*26)h
27a	Male	1	3	Testing	Unknown	Episign screen	c.738C>A (p.Cys246*)

BA bi-allelic, MA mono-allelic, NA not applicable.

^aTET3-deficient pathogenic samples used to identify the final DNA methylation episignature.

^bConsidered mono-allelic because only the c.3265G>A (p.Val1089Met) variant reduced catalytic activity in vitro, suggesting pathogenicity; c.2254C>T (p.Arg752Cys) did not reduce catalytic activity in vitro (ref. ⁸), suggesting non-pathogenicity.

^cVariants previously tested in our in vitro assay (ref. ⁸).

^dUnaffected daughter of Sample 5 and sister of Sample 4.

^eUnaffected son of 25 and brother of 26.

^fUnaffected mother of Sample 4.

^gUnaffected sister of Sample 6 and daughter of Samples 11 and 14.

^hPreviously considered VUS because mother was not thought to be affected; upon further evaluation, she was noted to be affected (see text for details).