Table 1.

Potentially deleterious single nucleotide variants (SNVs) in the affected individuals (III.5, III.6) that are not present in the unaffected fathers (II.5, II.9)

Chr	Position	Ref. Base	Var. Base	Mut type	Gene symbol	AA Subst	PhyloP44	Grant-ham	pph2 Prob.	SIFT score
2	204 443 623	A	G	het	CTLA4	Y60C	0.67	194	1.00	0.00
5	135 314 912	C	T	het	LECT2	G63E	4.06	98	1.00	0.00
5	149 340 131	C	G	het	SLC26A2	S261C	5.42	112	1.00	0.01
10	126 162 711	C	T	het	LHPP	R47W	1.09	101	0.94	0.03
11	63 039 655	C	T	het	LGALS12	T253I	−0.37	89	0.88	0.02
12	55 268 352	C	T	het	RBMS2	P357L	3.32	98	0.92	0.00
15	89 221 193	G	A	het	FURIN	G146S	5.00	56	0.98	0.01
16	86 321 735	A	C	het	KLHDC4	S175A	2.83	99	0.61	0.01
17	32 025 571	T	A	het	DHRS11	C69S	4.50	112	1.00	0.01
19	17 981 660	G	A	het	ARRDC2	V216M	0.75	21	0.99	0.01
19	19 029 430	C	T	het	ARMC6	A475V	1.40	64	0.99	0.00
20	2 725 075	G	A	het	CPXM1	R354C	6.47	180	1.00	0.00
20	4 653 387	C	T	het	PRND	R64C	0.56	180	1.00	0.00
21	45 521 464	C	T	het	POFUT2	A243T	4.91	58	0.99	0.01

Only novel SNVs with in silico predicted damaging effects (PolyPhen probability >0.50 and SIFT score ≤0.05 etc) are shown. No homozygous or compound heterozygous variants applying to these criteria were identified. For further details on SNV filtering, see the Methods section. Positions are according to hg18.

Highlighted in bold is the CTLA4 variant discussed in the manuscript.

Chr, chromosome; Ref., reference; Var., variant; Mut., mutation; AA subst., amino acid substitution; pph2 Prob., PolyPhen 2 probability.