File S1: Supplemental Information: List of 89 potential XLID genes
  The following list presents the 89 genes that were found to be mutated in our XLID cohort after application of the Combined Filter. Genes were prioritized by presence of a missense, nonsense, or splicing mutation. Weight was given for nonsense and splicing mutations. Weight was given for mutations present in both siblings.
  An asterisk (*) after the Gene ID indicates that the gene has been previously associated with XLID. The current list of XLID genes as of this publication stands at 103 (see bottom). Our target-enrichment system targets 975 chromosome X genes.
  Of the 89 genes in the list, 24 have been previously associated to XLID. This reflects a statistically significant 2.55-fold enrichment for known or previously associated XLID genes (p < 1E-5, hypergeometric test).

Gene ID		Priority
ZC4H2*		5
ATRX*		5
DMD*		4
UBE2A*		4
MAGEC1		4
FLNA*		3
PLXNA3		3
TAF1		3
TRO		3
HCFC1*		2
HUWE1*		2
MAOA*		2
ZNF711*		2
RBM10*		2
PLP1*		2
OTC*		2
ZMYM3		2
RNF128		2
ZRSR2		2
EFNB1		2
NHSL2		2
ZMAT1		2
GABRE		2
PRICKLE3	2
HAUS7		2
USP51		2
BCORL1		2
GRIPAP1		2
MXRA5		2
FHL1		2
GPC4		2
HSFX1,HSFX2	2
NXF4		2
CSAG1		2
SAGE1		2
FMR1*		1
MED12*		1
MECP2*		1
NHS*		1
OPHN1*		1
PGK1*		1
IDS*		1
SLC16A2*	1
MID1*		1
NSDHL*		1
ARHGEF9*	1
CLIC2*		1
USP9X		1
SMARCA1		1
MED14		1
USP26		1
COL4A5		1
FRMD7		1
SRPK3		1
AMER1		1
ALG13		1
MAGIX		1
SRPX		1
LAS1L		1
KAL1		1
CLCN4		1
TLR8		1
PHKA2		1
WBP5		1
APLN		1
GPR101		1
MCF2		1
HS6ST2		1
ATP11C		1
ZNF185		1
OGT		1
AIFM1		1
CFP		1
ZNF630		1
GUCY2F		1
PASD1		1
CHM		1
UBA1		1
NKAP		1
ATP1B4		1
MAMLD1		1
FAM47C		1
RPS4X		1
SUV39H1		1
NAP1L3		1
FAM9A		1
FAM47A		1
LOC100996648	1
MAGEA10		1


*103 known/associated XLID genes: ABCD1, ACSL4, AFF2, AGTR2, AP1S2, ARHGEF6, ARHGEF9, ARX, ATP6AP2, ATP7A, ATRX, BCOR, BRWD3, CASK, CCDC22, CDKL5, CLIC2, CUL4B, DCX, DKC1, DLG3, DMD, FANCB, FGD1, FLNA, FMR1, FTSJ1, GDI1, GK, GPC3, GRIA3, HCCS, HCFC1, HDAC8, HPRT, HSD17B10, HUWE1, IDS, IGBP1, IKBKG, IL1RAPL1, IQSEC2, KDM5C, KIAA2022, KLF8, SHROOM4, L1CAM, LAMP2, MAGT1, MAOA, MBTPS2, MECP2, MED12, MID1, MTM1, NAA10, NDP, NDUFA1, NHS, NLGN3, NLGN4, NSDHL, NXF5, OCRL, OFD1, OPHN1, OTC, PAK3, PCDH19, PDHA1, PGK1, PHF6, PHF8, PLP1, PORCN, PQBP1, PRPS1, PTCHD1, RAB39B, RBM10, RPL10, RPS6KA3, SIZN1, SLC16A2, SLC6A8, SLC9A6, SMC1A, SMS, SOX3, SRPX2, SYN1, SYP, TIMM8A, TSPAN7, UBE2A, UPF3B, ZC4H2, ZDHHC9, ZDHHC15, ZNF41, ZNF674, ZNF711, ZNF81