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VARIANT EFFECT	FUNCTIONAL CLASS	IMPACT
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Genes:
AIFM1, AKAP17A, AMOT, APLN, AR, ARHGAP4, ARL13A, ARMCX2, ARMCX4, ARSD, ARSE, ARSF, ARSH, ASMTL, ATP11C, ATP2B3, ATP7A, BCOR, BCORL1, BGN, BRWD3, BTK, C1GALT1C1, CA5B, CCDC160, CD99, CHM, CITED1, COL4A6, CPXCR1, CSF2RA, CT45A5, CXorf21, CXorf24, CXorf28, CXorf38, CXorf40A, CXorf56, CXorf58, CXorf65, CXorf67, CYSLTR1, DCAF8L2, DHRSX, DKC1, DLG3, DMD, DOCK11, EDA2R, EIF2S3, F9, FAAH2, FAM104B, FAM120C, FAM127B, FAM47A, FAM47B, FAM58A, FGF13, FLNA, FMR1, FOXR2, GABRE, GDI1, GDPD2, GLRA4, GPC4, GPR112, GPR174, GPR50, GRIA3, GRIPAP1, GTPBP6, GUCY2F, GYG2, H2BFM, H2BFWT, HDHD1, HDX, HEPH, HUWE1, IDS, IGSF1, IL1RAPL2, IL3RA, IRAK1, ITIH6, JADE3, KDM5C, KIAA1210, KIF4A, LCA10, LONRF3, MAGEA10, MAGEA11, MAGEA12, MAGEB10, MAGEB16, MAGEB2, MAGEB3, MAGEB4, MAGEC1, MAGEC2, MAGEC3, MAGED2, MAGEH1, MAGIX, MAMLD1, MAOA, MAOB, MAP7D2, MCF2, MED12, MPP1, MTMR1, MXRA5, NHS, NHSL2, NR0B1, NRK, NSDHL, NUDT10, NUDT11, NXF5, OTC, P2RY8, PAGE2, PAGE3, PASD1, PDHA1, PIN4, PIR, PLCXD1, PLXNB3, PNMA3, POF1B, POU3F4, PPP2R3B, PRKX, PRPS2, PRRG3, RAB40A, RAI2, RBM3, RBMX, RBMXL3, RGAG4, RIBC1, RPS4X, RPS6KA3, SATL1, SERPINA7, SHROOM2, SHROOM4, SLC25A5, SLC9A7, SLITRK2, SPANXC, SPANXD, SPANXN5, SPRY3, SRPK3, SSX5, SSX7, SYN1, SYTL4, SYTL5, TAB3, TAF7L, TCEAL2, TCEAL4, TCEAL6, TCEANC, TEX11, TEX13A, TGIF2LX, TLR8, TNMD, U82695.9, UBA1, UBE2NL, UPRT, VBP1, VCX, VCX2, VCX3A, VGLL1, VMA21, WDR13, WWC3, XAGE3, XG, ZBED1, ZBTB33, ZCCHC16, ZMAT1, ZNF280C, ZXDB,

+ Genes associated with diseases 48

Genes at Omim

AIFM1, AR, ARSE, ATP11C, ATP2B3, ATP7A, BCOR, BGN, BRWD3, BTK, C1GALT1C1, CHM, COL4A6, CSF2RA, CXorf56, DKC1, DLG3, DMD, EIF2S3, F9, FAM58A, FLNA, FMR1, GDI1, GRIA3, HUWE1, IDS, IGSF1, KDM5C, KIF4A, MAGED2, MAMLD1, MAOA, MED12, NHS, NR0B1, NSDHL, OTC, PDHA1, POU3F4, RBMX, RPS6KA3, SHROOM4, SYN1, TEX11, UBA1, VMA21, XG,

AIFM1	Combined oxidative phosphorylation deficiency 6, 300816 (3) Cowchock syndrome, 310490 (3) Deafness, X-linked 5, 300614 (3)
AR	Androgen insensitivity, 300068 (3) Androgen insensitivity, partial, with or without breast cancer, 312300 (3) Hypospadias 1, X-linked, 300633 (3) {Prostate cancer, susceptibility to}, 176807 (3) Spinal and bulbar muscular atrophy of Kennedy, 313200 (3)
ARSE	Chondrodysplasia punctata, X-linked recessive, 302950 (3)
ATP11C	?Hemolytic anemia, congenital, X-linked, 301015 (3)
ATP2B3	?Spinocerebellar ataxia, X-linked 1, 302500 (3)
ATP7A	Menkes disease, 309400 (3) Occipital horn syndrome, 304150 (3) Spinal muscular atrophy, distal, X-linked 3, 300489 (3)
BCOR	Microphthalmia, syndromic 2, 300166 (3)
BGN	Meester-Loeys syndrome, 300989 (3) Spondyloepimetaphyseal dysplasia, X-linked, 300106 (3)
BRWD3	Mental retardation, X-linked 93, 300659 (3)
BTK	Agammaglobulinemia, X-linked 1, 300755 (3) Isolated growth hormone deficiency, type III, with agammaglobulinemia, 307200 (3)
C1GALT1C1	Tn polyagglutination syndrome, somatic, 300622 (3)
CHM	Choroideremia, 303100 (3)
COL4A6	?Deafness, X-linked 6, 300914 (3)
CSF2RA	Surfactant metabolism dysfunction, pulmonary, 4, 300770 (3)
CXorf56	?Mental retardation, X-linked 107, 301013 (3)
DKC1	Dyskeratosis congenita, X-linked, 305000 (3)
DLG3	Mental retardation, X-linked 90, 300850 (3)
DMD	Becker muscular dystrophy, 300376 (3) Cardiomyopathy, dilated, 3B, 302045 (3) Duchenne muscular dystrophy, 310200 (3)
EIF2S3	MEHMO syndrome, 300148 (3)
F9	Hemophilia B, 306900 (3) {Warfarin sensitivity}, 122700 (3) Thrombophilia, X-linked, due to factor IX defect, 300807 (3) {Deep venous thrombosis, protection against}, 300807 (3)
FAM58A	STAR syndrome, 300707 (3)
FLNA	Frontometaphyseal dysplasia 1, 305620 (3) Cardiac valvular dysplasia, X-linked, 314400 (3) Heterotopia, periventricular, 1, 300049 (3) Congenital short bowel syndrome, 300048 (3) Intestinal pseudoobstruction, neuronal, 300048 (3) Melnick-Needles syndrome, 309350 (3) ?FG syndrome 2, 300321 (3) Otopalatodigital syndrome, type I, 311300 (3) Otopalatodigital syndrome, type II, 304120 (3) Terminal osseous dysplasia, 300244 (3)
FMR1	Fragile X syndrome, 300624 (3) Fragile X tremor/ataxia syndrome, 300623 (3) Premature ovarian failure 1, 311360 (3)
GDI1	Mental retardation, X-linked 41, 300849 (3)
GRIA3	Mental retardation, X-linked 94, 300699 (3)
HUWE1	Mental retardation, X-linked syndromic, Turner type, 300706 (3)
IDS	Mucopolysaccharidosis II, 309900 (3)
IGSF1	Hypothyroidism, central, and testicular enlargement, 300888 (3)
KDM5C	Mental retardation, X-linked, syndromic, Claes-Jensen type, 300534 (3)
KIF4A	?Mental retardation, X-linked 100, 300923 (3)
MAGED2	Bartter syndrome, type 5, antenatal, transient, 300971 (3)
MAMLD1	Hypospadias 2, X-linked, 300758 (3)
MAOA	Brunner syndrome, 300615 (3) {Antisocial behavior}, 300615 (3)
MED12	Lujan-Fryns syndrome, 309520 (3) Ohdo syndrome, X-linked, 300895 (3) Opitz-Kaveggia syndrome, 305450 (3)
NHS	Cataract 40, X-linked, 302200 (3) Nance-Horan syndrome, 302350 (3)
NR0B1	Adrenal hypoplasia, congenital, 300200 (3) 46XY sex reversal 2, dosage-sensitive, 300018 (3)
NSDHL	CK syndrome, 300831 (3) CHILD syndrome, 308050 (3)
OTC	Ornithine transcarbamylase deficiency, 311250 (3)
PDHA1	Pyruvate dehydrogenase E1-alpha deficiency, 312170 (3)
POU3F4	Deafness, X-linked 2, 304400 (3)
RBMX	?Mental retardation, X-linked, syndromic 11, Shashi type, 300238 (3)
RPS6KA3	Coffin-Lowry syndrome, 303600 (3) Mental retardation, X-linked 19, 300844 (3)
SHROOM4	Stocco dos Santos X-linked mental retardation syndrome, 300434 (3)
SYN1	Epilepsy, X-linked, with variable learning disabilities and behavior disorders, 300491 (3)
TEX11	Spermatogenic failure, X-linked, 2, 309120 (3)
UBA1	Spinal muscular atrophy, X-linked 2, infantile, 301830 (3)
VMA21	Myopathy, X-linked, with excessive autophagy, 310440 (3)
XG	[Blood group, XG system] (3)

Genes at Clinical Genomics Database

AIFM1, AR, ARSE, ATP2B3, ATP7A, BCOR, BRWD3, BTK, CHM, COL4A6, CSF2RA, DKC1, DLG3, DMD, F9, FAM58A, FLNA, FMR1, GDI1, GRIA3, HUWE1, IDS, IGSF1, KDM5C, KIF4A, MAGED2, MAMLD1, MAOA, MED12, NHS, NR0B1, NSDHL, NXF5, OTC, PDHA1, POF1B, POU3F4, RBMX, RPS6KA3, SERPINA7, SHROOM4, SYN1, TEX11, UBA1, VMA21, XG,

AIFM1	Deafness, X-linked 5
AR	Androgen insensitivity Androgen insensitivity, partial
ARSE	Chondrodysplasia punctata 1, X-linked recessive
ATP2B3	Spinocerebellar ataxia, X-linked 1
ATP7A	Menkes disease
BCOR	Microphthalmia, syndromic 2 Oculofaciocardiodental syndrome
BRWD3	Mental retardation, X-linked 93
BTK	Agammaglobulinemia, X-linked Agammaglobulinemia and isolated hormone deficiency Hypogammaglobulinemia, X-linked
CHM	Choiroideremia
COL4A6	Deafness, X-linked, with cochlear malformation
CSF2RA	Surfactant metabolism dysfunction, pulmonary, 4
DKC1	Dyskeratosis congenita, X-linked Hoyeraal-Hreidarsson syndrome
DLG3	Mental retardation, X-linked 90
DMD	Duchenne muscular dystrophy Becker muscular dystrophy Cardiomyopathy, dilated, 3B
F9	Hemophilia B Thrombophilia, X-linked, due to factor IX defect Warfarin sensitivity
FAM58A	STAR syndrome Toe syndactyly, telecanthus, and anogenital and renal malformations
FLNA	Cardiac valvular dysplasia, X-linked Heterotopia, periventricular, Ehlers-Danlos variant Intestinal pseudoobstruction, neuronal, X-linked/Congenital short bowel syndrome
FMR1	Premature ovarian failure
GDI1	Mental retardation, X-linked 41
GRIA3	Mental retardation, X-linked 94
HUWE1	Mental retardation, X-linked syndromic, Turner type
IDS	Mucopolysaccharidosis type II
IGSF1	Central hypothyroidism and testicular enlargement
KDM5C	Mental retardation, X-linked, syndromic, Claes-Jensen type
KIF4A	Mental retardation, X-linked 100
MAGED2	Bartter syndrome type 5, antenatal transient
MAMLD1	Hypospadias 2, X-linked
MAOA	Brunner syndrome
MED12	Lujan-Fryns syndrome Opitz-Kaveggia syndrome Mental retardation, X-linked, with Marfanoid habitus FG syndrome Ohdo syndrome
NHS	Nance-Horan syndrome Cataract 40
NR0B1	Adrenal hypoplasia, congenital 46,XY sex reversal 2
NSDHL	Congenital hemidysplasia with ichthyosiform erythroderma and limb defects (CHILD syndrome) CK syndrome
NXF5	Familial heart block and focal segmental glomerulosclerosis
OTC	Ornithine transcarbamylase deficiency
PDHA1	Pyruvate dehydrogenase E1-alpha deficiency Leigh syndrome, X-linked
POF1B	Premature ovarian failure 2B
POU3F4	Deafness, X-linked 2
RBMX	Mental retardation, X-linked, syndromic 11, Shashi type
RPS6KA3	Coffin-Lowry syndrome Mental retardation, X-linked 19
SERPINA7	Thyroxine-binding globulin deficiency Thyroxine-binding globulin excess
SHROOM4	Stocco dos Santos X-linked mental retardation syndrome
SYN1	Epilepsy, X-linked, with variable learning disabilities and behavior disorders
TEX11	Spermatogenic failure, X-linked 2
UBA1	Spinal muscular atrophy, X-linked 2, infantile
VMA21	Myopathy, X-linked, with excessive autophagy
XG	XG blood group

Genes at HGMD

Summary

Number of Variants: 2131
Number of Genes: 198

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AIFM1
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs1139851 dbSNP Clinvar	129283520	2411.76	A	G	PASS	1/1	58	SYNONYMOUS_CODING	LOW	None	0.49113	0.49110	0.49020				None None	None None None None	AIFM1\|0.770044974\|6.56%
AKAP17A
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs28661622 dbSNP Clinvar	1719897	3720.99	C	G	PASS	0/1	94	NON_SYNONYMOUS_CODING	MODERATE	None	0.53355	0.53350	0.48013	0.48	0.00		None None	None None None None	AKAP17A\|0.002882858\|88.87%
AMOT
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs147791784,rs373265985 dbSNP Clinvar	112022297	3280.79	C	CAGG	PASS	1/1	85	CODON_INSERTION	MODERATE	None	0.04079	0.04079	0.06154				None None	None None None None	AMOT\|0.349674275\|24.15%
APLN
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs3115758 dbSNP Clinvar	128781864	1393.19	C	A	PASS	1/1	50	NON_SYNONYMOUS_CODING	MODERATE	None	0.46861	0.46860		1.00	0.00		None None	None None None None	APLN\|0.015985441\|76.47%
AR
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs780052930 dbSNP Clinvar	66766356	254.3	TG...	TG...	PASS	1/1	1	CODON_CHANGE_PLUS_CODON_INSERTION	MODERATE	None			0.07586				None None	None None None None	AR\|0.999436019\|0.35%
ARHGAP4
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs62620965 dbSNP Clinvar	153176284	1387.15	C	T	PASS	1/1	47	SYNONYMOUS_CODING	LOW	None	0.02040	0.02040	0.05486				None None	None None None None	ARHGAP4\|0.028368935\|70.27%
ARL13A
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs6523438 dbSNP Clinvar	100245606	3278.86	A	G	PASS	1/1	112	None	None	None	0.85642	0.85640	0.16250				None None	None None None None	ARL13A\|0.006011211\|84.59%
	View	combined sample_42.variant6	X	rs3934462 dbSNP Clinvar	100243459	2205.87	G	T	PASS	1/1	51	NON_SYNONYMOUS_CODING	MODERATE	None	0.91338	0.91340	0.10304	0.12	0.00		None None	None None None None	ARL13A\|0.006011211\|84.59%
ARMCX2
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs3850315 dbSNP Clinvar	100911066	2007.54	C	T	PASS	1/1	74	SYNONYMOUS_CODING	LOW	None	0.96689	0.96690	0.05737				None None	None None None None	ARMCX2\|0.023937868\|72.22%
ARMCX4
Omim - GeneCards - NCBI
	Options	Individual	Chr	RsId	Pos	Qual	Ref	Alt	Filter	Gen	Read Depth	Effect	Impact	Func Class	1kgenomes	dbSNP	ESP6500	Sift	PP2	CADD	M-CAP	CLINVAR	HI Score
	View	combined sample_42.variant6	X	rs963618 dbSNP Clinvar	100743037	1996.69	C	T	PASS	1/1	88	START_GAINED	LOW	None	0.65987	0.65990					None None	None None None None	ARMCX4\|0.006015436\|84.57%
	View	combined sample_42.variant6	X	rs61736018 dbSNP Clinvar	100747694	2381.07	G	C	PASS	1/1	59	NON_SYNONYMOUS_CODING	MODERATE	None	0.17378	0.17380			0.69		None None	None None None None	ARMCX4\|0.006015436\|84.57%
	View	combined sample_42.variant6	X	rs5951332 dbSNP Clinvar	100743826	2206.21	A	G	PASS	1/1	98	NON_SYNONYMOUS_CODING	MODERATE	None	0.61934	0.61930			0.00		None None	None None None None	ARMCX4\|0.006015436\|84.57%
	View	combined sample_42.variant6	X	rs73563076 dbSNP Clinvar	100747453	2985.69	G	A	PASS	1/1	70	NON_SYNONYMOUS_CODING	MODERATE	None	0.08715	0.08715			0.14		None None	None None None None	ARMCX4\|0.006015436\|84.57%