Table 1. Overview of sequence variants identified in 248 index patients with XLID.

Variant class	Variants found in the study cohort and present in control populationsa			Variants found in the study cohort and absent in control populationsa
	Recurrent	Non-recurrent	Total	Recurrent	Non-recurrent	Total
Synonymous	602	262	864	9	235	244
Missense	606	356	962	15 (1)	461 (9)	476
Non-sense	6	4	10	0	13	13
In-frame indels (<50 kb)	13	4	17	1	18 (1)	19
Small frameshift indels (⩽50 kb)	12	7	19	3	29 (1)	32
Large indels (>50 kb)	0	0	0	0	9b	9
Total	1239	633	1872	28	765	793
Canonical splice sites	7	3	10	2	10	12
Retrocopies	0	0	0	3	5	8
Potential cryptic splice sites	0	0	0	0	4	4
Non-coding exons	2132	663	2795	342	1468	1810
Total	3378	1299	4677	375	2252	2627

Abbreviations: HGMD, Human Gene Mutation Database; XLID, X-linked intellectual disability.

^aVariants present in HGMD with PubMed entries (numbers shown in parentheses) were treated as potentially disease relevant and therefore were excluded from filtering against control populations (dbSNP 135, Exome Variant Server, NHLBI Exome Sequencing Project (ESP), Seattle, WA, 1000 Genomes Project, 200 Danish exomes³). Indels=insertions and deletions.

^bThree duplications were only detected by using a Hidden–Markov Model-based method.³⁰