Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease

Table 3 Top ten candidate genes in the Schinzel-Giedion case study

Rank	Gene	Number of samples	Number of unique variants	Total number of variants	Haploinsufficiency prediction	Maximum Phylop (placental mammals)
1	SETBP1	4	2	3	0.721	3.455
2	CDC27	4	5	13	-	3.106
3	CTBP2	4	3	8	-	2.805
4	PRB1	4	2	5	-	1.458
5	KIR2DL1	4	1	2	-	1.05
6	FLG	4	5	6	-	1.034
7	OR11H1	4	0	1	-	0.856
8	KIR2DL3	4	4	6	-	-0.326
9	CDCP2	4	0	1	-	-0.365
10	NBPF12	4	0	2	-	-0.411

The data were analyzed using Annotate-it. Genes were considered a hit if they contained either nonsynonymous, nonsense or essential splice site variants that were not present in dbSNP or found in the 1000 Genomes Project. Genes were then sorted based on number of affected samples in which the gene was a candidate and conservation in placental mammals. Additionally, the total number of variants present across all samples and the number of variants unique to only one sample is given.

ISSN: 1756-994X