Table 1.

Rare variants segregating with sound–color synesthesia within each family

Family	Position	Ref/Alt	Gene	ExAC MAF	Impact	CADD	Eigen score	PolyPhen	SIFT
11	1:1231208	C/T	ACAP3	0.002	Missense	18.65	−0.59	Benign	Deleterious
2	1:146696486	C/G	FMO5	0	Splice donor	27.50	1.18	NA	NA
2	1:151665566	T/C	SNX27	0.005	Regulatory	1.22	0.42	NA	NA
2	1:154574699	T/G	ADAR	0	Missense	24.80	0.14	Possibly damaging	Deleterious
2	1:156899248	G/A	LRRC71	0.007	Intron	5.29	0.29	NA	NA
2	1:162760613	C/G	HSD17B7	0	Missense	29.00	0.80	Probably damaging	Deleterious
2	1:162825523	AGAG/A	C1orf110	0	Regulatory	14.18	NA	NA	NA
2,16	1:192321228	A/G	RGS21	0	Missense	25.30	0.98	Probably damaging	Deleterious
16	1:205899176	C/A	SLC26A9	0	Synonymous	11.48	1.43	NA	NA
16	3:10280460	A/G	IRAK2	0.002	Missense	17.57	−0.21	Benign	Tolerated
11	4:20619178	C/T	SLIT2*	0.005	Missense	22.50	−0.56	Benign	Tolerated
11	4:25667731	G/A	SLC34A2	NA	Intron	1.73	−0.037	NA	NA
2	4:72620719	G/A	GC	NA	Synonymous	0.39	−0.058	NA	NA
16	4:155511967	G/C	FGA	NA	Regulatory	0.94	0.65	NA	NA
16	5:1335280	G/A	CLPTM1L	0.003	Missense	28.60	0.23	Possibly damaging	Deleterious
16	5:16671591	G/A	MYO10*	0.006	Synonymous	13.99	1.56	NA	NA
2	5:44811207	T/G	MRPS30	0.003	Missense	28.10	0.73	Probably damaging	Deleterious
2	5:52347346	G/A	ITGA2*	NA	Missense	24.60	0.46	Probably damaging	Tolerated
2	5:64492917	A/G	ADAMTS6	0	Synonymous	3.33	1.50	NA	NA
2	7:140386681	G/A	ADCK2	NA	Upstream	0.78	−0.33	NA	NA
11	9:139342231	A/G	SEC16A	NA	Intron	1.72	−0.054	NA	NA
16	10:49937707	C/A	WDFY4	NA	Intron	10.42	0.16	NA	NA
11	11:124747839	G/T	ROBO3*	0.003	Missense	27.90	0.23	Probably damaging	Deleterious
11	12:30834682	G/A	IPO8	NA	Synonymous	15.41	0.72	NA	NA
11	12:49952781	G/A	MCRS1	0.01	Downstream	4.74	0.15	NA	NA
2	13:47263384	A/G	LRCH1	NA	Intron	3.22	−0.12	NA	NA
2	13:49710555	G/A	FNDC3A	0	Missense	33.00	0.72	Probably damaging	Deleterious
11	13:110866346	G/A	COL4A1*	0.004	Missense	26.50	0.72	NA	Deleterious
16	14:23848194	C/T	CMTM5	0	Downstream	7.20	0.43	NA	NA
2	16:71101385	G/A	HYDIN	NA	Intron	8.53	0.28	NA	NA
2	17:71354180	T/C	SDK2	0	Intron	1.60	−0.16	NA	NA
2	17:73832045	G/A	UNC13D	0	Intron	0.28	−0.079	NA	NA
11	17:80708522	A/C	FN3K	0.001	Missense	15.58	−0.49	Benign	Tolerated
11	19:44513250	C/T	ZNF230	0.007	Missense	0.73	−1.16	Benign	Tolerated
11	20:62867995	C/T	MYT1	0	Synonymous	11.20	1.14	NA	NA
2	22:17671193	G/A	CECR1	NA	Upstream	0.34	−0.39	NA	NA
11	X:135126891	A/T	SLC9A6*	0.003	3′ UTR	6.21	NA	NA	NA

ExAC, Exome Aggregation Consortium; PolyPhen, polymorphism phenotyping; Ref/Alt, reference/alternative; SIFT, sorting intolerant from tolerant.

^*Genes associated with axonogenesis (GO:0007409) and cell migration (GO:0016477), biological categories with relevance to the hyperconnectivity account of synesthesia.