Table 3. Summary of variant analysis and segregation with EA phenotype.

	Patient 1	Patient 2	Patient 3	Patient 4	Control 1	Control 2	All patients	Not in control
Q20 and 5x coverage	150980	141952	141305	119037	137102	142110	52560	1375
+Missense, nonsense, frameshift	10326	10391	10373	10132	10352	10320	5229	116
+Not in dbSNP (version 130)	1269	1319	1304	1258	1283	1319	289	20
+In candidate linkage regions	14	12	5	7	6	6	4	4
+Not in Irish control exomes	10	8	3	6	4	5	3	3
+Not in 1000 genomes or ESP	6	6	3	5	3	3	3	3

Exome sequencing of six family members, four with EA and two without EA identified multiple variants. Data were cleaned and filtered to include variants that were likely to alter protein function and structure, and not previously reported in dbSNP130. To identify candidate disease-causing variants, exome data were analyzed in conjunction with previous linkage analysis. Four variants within the linkage peaks were common to all patients with EA but absent in the unaffected family members. Three of these variants (in HSPG2, UBR4 and FCN3) were also absent in individuals in the Irish exome database. The variant in FCN3 has been previously reported and is not considered a disease-causing candidate variation. The data prioritization method supports the remaining variants as candidate variants for EA.