#gene_symbol entrez_id gene_name band description disorder omim_id omim_name inheritance level chromosome
DHCR7	1717	7-dehydrocholesterol reductase	11q13.4	Smith-Lemli-Opitz syndrome is an inborn error of metabolism affecting cholesterol biosynthesis. The rate of ASD in this syndrome is high: 53% (9/17) meet criteria for autism and 71% (10/14) have ASD, according to two studies	Smith-Lemli-Opitz syndrome	270400	Smith-Lemli-Opitz syndrome	AR	4	11
CACNA1C	775	calcium channel, voltage-dependent, L type, alpha 1C subunit	12p13.3	Timothy syndrome (long QT syndrome with syndactyly). Among 5 children with Timothy syndrome, 3 had autism, one had ASD, and one had severe language delay	Timothy syndrome	601005	Timothy syndrome	AD	4	12
UBE3A	7337	ubiquitin protein ligase E3A	15q11.2	Angelman syndrome is an imprinting disorder caused by maternal deletion of chromosome 15, paternal uniparental disomy, imprinting defect, or UBE3A mutation. Over one-half of the patients with Angelman syndrome have ASD	Angelman syndrome	105830	Angelman syndrome	AD	4	15
TSC2	7249	tuberous sclerosis 2	16p13.3	Tuberous sclerosis is caused by mutations in the TSC1 or TSC2 genes (see TSC1 above, 9q34.13)	Tuberous sclerosis	191100	Tuberous sclerosis-2	AD	4	16
FMR1	2332	fragile X mental retardation 1	Xq27.3	Fragile X syndrome is found in ~2% of individuals with ASD. ~60% of males with the full mutation have ASD, ~20% in females. The premutation is also associated with an increased risk of ASD: 10-15% in males, 5% in females	fragile X syndrome	300624	Fragile X syndrome	XL	4	X
MECP2	4204	methyl CpG binding protein 2 (Rett syndrome)	Xq28	MECP2 mutations or deletions cause Rett syndrome in females, and congenital encephalopathy or non-syndromic ID in males; MECP2 duplication syndrome, mostly in males	Rett syndrome	312750	Rett syndrome	XL	4	X
CNTNAP2	26047	contactin associated protein-like 2	7q35	Cortical dysplasia-focal epilepsy syndrome and Pitt-Hopkins-like syndrome-1 are autosomal recessive disorders. Deletions or chromosomal rearrangements disrupting a single copy of CNTNAP2 have been reported in patients with ASD, ID, epilepsy, schizophrenia and bipolar disorder as well as in healthy subjects; however, the clinical significance of the disruption of only one allele is unknown	Cortical dysplasia-focal epilepsy syndrome	610042	Cortical dysplasia-focal epilepsy syndrome	AR (AD too?)	4	7
TSC1	7248	tuberous sclerosis 1	9q34	Tuberous sclerosis is caused by mutations in the TSC1 or TSC2 genes. The frequency of tuberous sclerosis among patients with ASD in epidemiological samples is ~1%; the frequency of ASD in subjects with tuberous sclerosis varies between 16-60%	Tuberous sclerosis	191100	Tuberous sclerosis-1	AD	4	9
PTEN	5728	phosphatase and tensin homolog	10q23.3	PTEN hamartoma-tumor syndrome (including Bannayan-Riley-Ruvalcaba syndrome and Cowden syndrome); ID and ASD with macrocephaly. The frequency of PTEN mutations in children with ASD and macrocephaly is unknown; in one study, 15% (4/26) of children with PTEN mutations had ASD	PTEN hamartoma-tumor syndrome	601728	PTEN hamartoma-tumor syndrome	AD	3	10
IGF2	3481	insulin-like growth factor 2 (somatomedin A)	11p15.5	Aberrant imprinting of IGF2 is associated with Beckwith-Wiedermann syndrome and Silver-Russell syndrome, characterized by growth abnormalities. Both disorders have been reported in ASD; 7% (6/87) of children with Beckwith-Wiedermann syndrome have ASD	Beckwith-Wiedermann syndrome	130650	Beckwith-Wiedermann syndrome	AD	3	11
KRAS	3845	v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog	12p12.1	Cardio-facio-cutaneous syndrome	Cardio-facio-cutaneous syndrome	115150	Cardiofaciocutaneous syndrome	AD	3	12
CEP290	80184	centrosomal protein 290kDa	12q21.32	Joubert syndrome 5; Leber congenital amaurosis (see AHI1 above, 6q23.3)	Joubert syndrome 5	610188	Joubert syndrome 5	AR	3	12
PAH	5053	phenylalanine hydroxylase	12q22-q24.2	Phenylketonuria was identified as a cause of ASD in older studies, but it is no longer observed where neonatal testing exists	Phenylketonuria	261600	Phenylketonuria	AR	3	12
PTPN11	5781	protein tyrosine phosphatase, non-receptor type 11	12q24	Noonan syndrome (craniofacial anomalies, short stature, heart defects). In a sample of 65 children with Noonan syndrome, 8% had a diagnosis of ASD	Noonan syndrome	163950	Noonan syndrome 1	AD	3	12
FOXG1	2290	forkhead box G1	14q13	Deletions and mutations cause a congenital variant of Rett syndrome, duplications are associated with ID, severe speech delay, and epilepsy	Rett syndrome	613454	Rett syndrome, congenital variant	AD	3	14
MAP2K1	5604	mitogen-activated protein kinase kinase 1	15q22.1-q22.33	Cardio-facio-cutaneous syndrome	Cardio-facio-cutaneous syndrome	115150	Cardiofaciocutaneous syndrome	AD	3	15
CREBBP	1387	CREB binding protein	16p13.3	Rubinstein-Taybi syndrome (ID, characteristic facial features, broad thumbs and great toes). Mutations in EP300 can also cause Rubinstein-Taybi syndrome (in 3%) but have not been reported in ASD	Rubinstein-Taybi syndrome	180849	Rubinstein-Taybi syndrome	AD	3	16
RPGRIP1L	23322	RPGRIP1-like	16q12.2	Joubert syndrome 7, Meckel syndrome, COACH syndrome (Joubert syndrome with congenital hepatic fibrosis)	COACH syndrome	216360	COACH syndrome	AR	3	16
PAFAH1B1	5048	platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)	17p13.3	Deletions or point mutations of PAFAH1B1 (LIS1) result in isolated lissencephaly; extended deletions including YWHAE cause Miller-Dieker syndrome; microduplications of PAFAH1B1 cause ID and subtle brain abnormalities. 30% (12/40) of patients with PAFAH1B1 point mutations or intragenic deletions have moderate to severe autistic features	Lissencephaly 1	607432	Lissencephaly 1	AD	3	17
YWHAE	7531	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide	17p13.3	Deletions including YWHAE are associated with Miller-Dieker syndrome, a contiguous gene syndrome; YWHAE is thought to be responsible for the more severe brain phenotype compared to deletions affecting only PAFAH1B1; 17p13.3 microduplications mapping to the Miller-Dieker critical region have also been identified. Only microduplications have been reported in ASD	Miller-Dieker syndrome	247200	Miller-Dieker lissencephaly syndrome	AD	3	17
RAI1	10743	retinoic acid induced 1	17p11.2	Deletions or mutations of RAI1 cause Smith-Magenis syndrome; duplications result in Potocki-Lupski syndrome. ASDs are observed frequently in both syndromes	Smith-Magenis syndrome	182290	Smith-Magenis syndrome	AD	3	17
RNF135	84282	ring finger protein 135	17q11.2	Mutations in RNF135, which is within the NF1 microdeletion region, cause overgrowth, ID, and dysmorphic features, demonstrating that haploinsufficiency of RNF135 contributes to the phenotype of NF1 microdeletion cases	overgrowth ID	611358	Overgrowth syndrome	AD	3	17
NF1	4763	neurofibromin 1	17q11.2	Neurofibromatosis type 1. The frequency of neurofibromatosis among patients with ASD is ~0.5%; the frequency of ASD in subjects with neurofibromatosis is 4% (3/74)	Neurofibromatosis type 1	162200	Neurofibromatosis, type 1	AD	3	17
SGSH	6448	N-sulfoglucosamine sulfohydrolase	17q25.3	Sanfilippo syndrome A (mucopolysaccharidosis III A)	Sanfilippo syndrome A	252900	Mucopolysaccharidisis type IIIA (Sanfilippo A)	AR	3	17
NFIX	4784	nuclear factor I/X (CCAAT-binding transcription factor)	19p13.3	Sotos-like overgrowth syndrome with advanced bone age, macrocephaly, ID, scoliosis, and unusual facial features	Sotos-like overgrowth syndrome	117550	Sotos syndrome	AD	3	19
GAMT	2593	guanidinoacetate N-methyltransferase	19p13.3	Guanidine acetate methyltransferase (GAMT) deficiency (brain creatine deficiency, synthesis defect)	Guanidine acetate methyltransferase (GAMT) deficiency	612736	GAMT deficiency	AR	3	19
DMPK	1760	dystrophia myotonica-protein kinase	19q13.3	Myotonic dystrophy 1 (Steinert disease). In a study of 57 children and adolescents with myotonic dystrophy 1, 49% had ASD (including 35% with autism). Several individuals with Asperger syndrome have been reported	Myotonic dystrophy 1 (Steinert disease)	160900	Myotonic dystrophy 1	AD	3	19
MKKS	8195	McKusick-Kaufman syndrome	20p12	Bardet-Biedl syndrome is a ciliopathy, like Joubert syndrome	Bardet-Biedl syndrome	209900	Bardet-Biedl syndrome 6	AR	3	20
TBX1	6899	T-box 1	22q11.21	22q11 deletion syndrome phenotype (velocardiofacial/DiGeorge syndrome);22% (9/41) patients with velocardiofacial syndrome also have ASD	22q11 deletion syndrome phenotype	192430	Velocardiofacial syndrome	AD	3	22
ADSL	158	adenylosuccinate lyase	22q13.1|22q13.2	Adenylosuccinate lyase deficiency; ~50% present autism/autistic features	Adenylosuccinate lyase deficiency	103050	Adenylosuccinase deficiency	AR	3	22
SHANK3	85358	SH3 and multiple ankyrin repeat domains 3	22q13.3	22q13 deletion syndrome (Phelan-McDermid syndrome) is caused by deletions of SHANK3; ASD or autistic features are frequent. SHANK3 mutations have also been reported in individuals with ASD	22q13 deletion syndrome	606232	Chromosome 22q13.3 deletion syndrome	AD	3	22
NLGN4X	57502	neuroligin 4, X-linked	Xp22.33	Non-syndromic X-linked ID and/or ASD; both mutations and deletions have been reported	X-linked Mental retardation	300495	Mental retardation, X-linked	XL	3	X
MID1	4281	midline 1 (Opitz/BBB syndrome)	Xp22	Opitz syndrome (Opitz/BBB syndrome)	Opitz syndrome	300000	Opitz G syndrome, type I	XL	3	X
NHS	4810	Nance-Horan syndrome (congenital cataracts and dental anomalies)	Xp22.13	Nance-Horan syndrome (congenital cataracts and dental anomalies)	Nance-Horan syndrome	302350	Nance-Horan syndrome	XL	3	X
CDKL5	6792	cyclin-dependent kinase-like 5	Xp22	Rett-like syndrome with infantile spasms and severe ID in female patients	infantile spasms	300672	Epileptic encephalopathy, early infantile, 2	XL	3	X
ARX	170302	aristaless related homeobox	Xp21	Large spectrum of ID phenotypes, including X-linked lissencephaly and abnormal genitalia, West syndrome, Partington syndrome, and non-syndromic ID	X-linked mental retardation	300419	Mental retardation, X-linked 36/43/54	XL	3	X
IL1RAPL1	11141	interleukin 1 receptor accessory protein-like 1	Xp22.1-p21.3	Non-syndromic X-linked ID and/or ASD	X-linked mental retardation	300143	Mental retardation, X-linked, 21/34	XL	3	X
DMD	1756	dystrophin	Xp21.2	Muscular dystrophy, Duchenne and Becker types; in one study, 19% (16/85) met criteria for ASD	Duchenne muscular dystrophy	310200	Duchenne muscular dystrophy	XL	3	X
NDP	4693	Norrie disease (pseudoglioma)	Xp11.4	Norrie disease (occuloacousticocerebral dysplasia)	Norrie disease	310600	Norrie disease	XL	3	X
PQBP1	10084	polyglutamine binding protein 1	Xp11.23	Large spectrum of ID phenotypes, including Renpenning syndrome (microcephaly, short stature, small testes and dysmorphic features) and non-syndromic ID	Renpenning syndrome	309500	Renpenning syndrome	XL	3	X
FTSJ1	24140	FtsJ homolog 1 (E. coli)	Xp11.23	Non-syndromic X-linked ID	Non-syndromic X-linked ID	309549	Mental retardation, X-linked-9	XL	3	X
CACNA1F	778	calcium channel, voltage-dependent, L type, alpha 1F subunit	Xp11.23	X-linked incomplete congenital stationary night blindness, severe form	X-linked incomplete congenital stationary night blindness (CSNB2)	300071	Night blindness, congenital stationary, X-linked, type 2A	XL	3	X
IQSEC2	23096	IQ motif and Sec7 domain 2	Xp11.22	Non-syndromic X-linked ID; mutations in 4 large pedigrees, 2 of which include individuals with ASD/autistic traits	Non-syndromic X-linked ID	309530	Mental retardation, X-linked 1	XL	3	X
FGD1	2245	FYVE, RhoGEF and PH domain containing 1	Xp11.21	Aarskog-Scott syndrome (faciogenital dysplasia); non-syndromic X-linked ID. Four cases with a clinical diagnosis of Aarskog-Scott syndrome and ASD/autistic features have been described (not confirmed molecularly)	Aarskog-Scott syndrome	305400	Aarskog-Scott syndrome	XL	3	X
OPHN1	4983	oligophrenin 1	Xq12	ID with cerebellar and vermis hypoplasia	XLMR with cerebellar hypoplasia and distinctive facial appearance	300486	Mental retardation, X-linked, with cerebellar hypoplasia and distinctive facial appearance	XL	3	X
MED12	9968	mediator complex subunit 12	Xq13	Lujan-Fryns syndrome (X-linked ID with marfanoid habitus); 62.5% (20/32) of subjects with Lujan-Fryns syndrome have an autistic-like disorder	Lujan-Fryns syndrome	309520	Lujan-Fryns syndrome	XL	3	X
ATRX	546	alpha thalassemia/mental retardation syndrome X-linked	Xq21.1	Large spectrum of phenotypes including ATRX syndrome (alpha thalassemia/mental retardation syndrome X-linked) and non-syndromic X-linked ID	ATRX syndrome	301040	Alpha-thalassemia/mental retardation syndrome	XL	3	X
PCDH19	57526	protocadherin 19	Xq13.3	X-linked female-limited epilepsy and cognitive impairment; ASD/autistic features are common: 22% (6/27) and 38% (5/13) in two studies	Sporadic infantile epileptic encephalopathy	300088	Epileptic encephalopathy, early infantile, 9	XL	3	X
ACSL4	2182	acyl-CoA synthetase long-chain family member 4	Xq22.3-q23	Non-syndromic X-linked ID	Non-syndromic X-linked ID	300387	Mental retardation, X-linked nonspecific, 63	XL	3	X
DCX	1641	doublecortin	Xq22.3-q23	Type 1 lissencephaly	Type 1 lissencephaly	300067	Lissencephaly, X-linked	XL	3	X
AGTR2	186	angiotensin II receptor, type 2	Xq22-q23	Non-syndromic X-linked ID	Non-syndromic X-linked ID	300852	Mental retardation, X-linked 88	XL	3	X
UPF3B	65109	UPF3 regulator of nonsense transcripts homolog B (yeast)	Xq25-q26	Non-syndromic X-linked ID with or without autism	Non-syndromic X-linked ID	300676	Mental retardation, X-linked, syndromic 14	XL	3	X
GRIA3	2892	glutamate receptor, ionotrophic, AMPA 3	Xq25	Non-syndromic X-linked ID; mutations as well as 3 cases of partial duplication of GRIA3 have been reported in patients with autism or autistic behavior	Non-syndromic X-linked ID	300699	Mental retardation, X-linked 94	XL	3	X
OCRL	4952	oculocerebrorenal syndrome of Lowe	Xq25	Lowe syndrome or oculo-cerebro-renal syndrome (ID, bilateral cataract and renal Fanconi syndrome)	Lowe syndrome	309000	Lowe syndrome	XL	3	X
SLC9A6	10479	solute carrier family 9 (sodium/hydrogen exchanger), member 6	Xq26.3	Syndromic X-linked ID, Christianson type (ID, microcephaly, epilepsy, and ataxia)	mental retardation, microcephaly, epilepsy, and ataxia	300243	Mental retardation, X-linked syndromic, Christianson type	XL	3	X
ARHGEF6	9459	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	Xq26.3	Non-syndromic X-linked ID	X-linked forms of mental retardation	300436	Mental retardation, X-linked nonspecific, type 46	XL	3	X
AFF2	2334	AF4/FMR2 family, member 2	Xq28	Fragile X mental retardation 2 (FRAXE)	Fragile X mental retardation 2 (FRAXE)	309548	Mental retardation, X-linked, FRAXE type 	XL	3	X
SLC6A8	6535	solute carrier family 6 (neurotransmitter transporter, creatine), member 8	Xq28	Creatine deficiency syndrome; non-syndromic ID. Brain creatine deficiency can be caused by mutation in the creatine transporter gene SLC6A8, or by defects in the biosynthesis of creatine (GAMT and GATM genes); mutations in all three genes have been reported in ASD; ASD/autistic features appear to be frequent in creatine deficiency syndromes	creatine transporter deficiency	300352	Creatine deficiency syndrome, X-linked	XL	3	X
L1CAM	3897	L1 cell adhesion molecule	Xq28	Syndromic X-linked ID, MASA (mental retardation, aphasia, shuffling gait, and adducted thumbs) syndrome	severe mental retardation, spastic paraparesis, adducted thumbs, agenesis of corpus callosum and microcephaly	303350	MASA syndrome	XL	3	X
RAB39B	116442	RAB39B, member RAS oncogene family	Xq28	X-linked ID associated with autism, epilepsy, and macrocephaly in two large pedigrees	X-linked mental retardation	300271	Mental retardation, X-linked-72 	XL	3	X
POMGNT1	55624	protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase	1p34.1	Muscle-eye-brain disease (congenital muscular dystrophy, structural eye abnormalities and lissencephaly)	Muscle-eye-brain disease (MEB)	253280	Muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 3	AR	3	1
RPE65	6121	retinal pigment epithelium-specific protein 65kDa	1p31	Leber congenital amaurosis	Leber congenital amaurosis	204100	Leber congenital amaurosis 2	AR	3	1
NRXN1	9378	neurexin 1	2p16.3	Disrupted in ASD, ID, and other neurodevelopmental and psychiatric disorders (autosomal dominant?); Pitt-Hopkins-like syndrome-2 (autosomal recessive)	Pitt-Hopkins-like mental retardation	600565	Pitt-Hopkins-like syndrome 2	AD?/AR (Pitt-Hopkins-like)	3	2
MBD5	55777	methyl-CpG binding domain protein 5	2q23.1	MBD5 is the only gene deleted in all subjects with the 2q23.1 microdeletion syndrome	2q23.1 microdeletion syndrome	156200	Mental retardation	AD	3	2
SCN1A	6323	sodium channel, voltage-gated, type I, alpha subunit	2q24.3	Severe myoclonic epilepsy of infancy (Dravet syndrome); ASD or autistic features have been reported repeatedly	Dravet syndrome	607208	Dravet syndrome	AD	3	2
SATB2	23314	SATB homeobox 2	2q33	Haploinsufficiency of SATB2 causes some of the clinical features of the 2q33.1 microdeletion syndrome, including severe ID, cleft palate and tooth anomalies. SATB2 was disrupted in an individual with ASD carrying a balanced translocation	2q33.1 microdeletion syndrome	119540	Cleft palate and mental retardation	AD	3	2
FOXP1	27086	forkhead box P1	3p14.1	Autosomal dominant non-syndromic ID and ASD; disrupted in two patients with ID and autism/ASD	sporadic nonsyndromic ID	613670	Mental retardation with language impairment and autistic features	AD	3	3
NIPBL	25836	Nipped-B homolog (Drosophila)	5p13.2	Cornelia de Lange syndrome (facial dysmorphism, upper limb malformations, growth and cognitive retardation) is caused by mutations in NIPBL (60%), SMC1A (5%), and SMC3 (1 patient). ASD has been reported in subjects with NIPBL and SMC1A mutations. 47-67% of individuals with de Lange syndrome have autism/ASD	Cornelia de Lange Syndrome	122470	Cornelia de Lange syndrome 1	AD	3	5
MEF2C	4208	myocyte enhancer factor 2C	5q14	MEF2C is responsible for the 5q14.3 microdeletion syndrome; both mutations and deletions have been described in individuals with ASD or autistic behavior	5q14.3 microdeletion syndrome	613443	Chromosome 5q14.3 deletion syndrome	AD	3	5
ALDH7A1	501	aldehyde dehydrogenase 7 family, member A1	5q31	Pyridoxine-dependent epilepsy (antiquitin deficiency) is a rare disorder characterized by early onset seizures that are controlled by pyridoxine (vitamin B6) Among 64 published ALDH7A1 mutations, at least 3 have been reported with autism or autistic features	Pyridoxine-dependent epilepsy	266100	Epilepsy, pyridoxine-dependent	AR	3	5
NSD1	64324	nuclear receptor binding SET domain protein 1	5q35	Sotos syndrome (overgrowth syndrome characterized by macrocephaly, advanced bone age, characteristic facial features and learning disabilities). The proportion of subjects with Sotos that have ASD is unknown, as only isolated cases have been reported	Sotos syndrome	117550	Sotos syndrome	AD	3	5
ALDH5A1	7915	aldehyde dehydrogenase 5 family, member A1	6p22	Succinic semialdehyde dehydrogenase deficiency (gamma-hydroxybutyric aciduria); 12% (4/33) have autistic features	Succinic semialdehyde dehydrogenase deficiency	271980	Succinic semialdehyde dehydrogenase deficiency	AR	3	6
AHI1	54806	Abelson helper integration site 1	6q23.3	Joubert syndrome 3. Joubert syndrome is a clinically and genetically heterogeneous group of ciliopathies characterized by cerebellar ataxia, ID and breathing abnormalities, sometimes including retinal dystrophy and renal disease. ASD is a relatively frequent finding in patients with Joubert syndrome, present in 13-36% of patients. Ten genes have been implicated in Joubert syndrome, but so far, only 4 have been reported to be mutated in subjects with ASD/autistic traits	Leber congenital amaurosis	204100	Leber congenital amaurosis 2	AR	3	6
HOXA1	3198	homeobox A1	7p15.3	HOXA1 syndrome, Bosley-Salih-Alorainy variant (horizontal gaze abnormalities, deafness, facial weakness, hypoventilation, cardiovascular malformations, ID and ASD); 2/9 patients meet criteria for autism	Bosley-Salih-Alorainy syndrome	601536	Bosley-Salih-Alorainy syndrome	AR	3	7
BRAF	673	v-raf murine sarcoma viral oncogene homolog B1	7q34	Cardio-facio-cutaneous syndrome is caused by gain of function mutations in KRAS, BRAF, MEK1, or MEK2. CFC syndrome shows phenotypic overlap with Noonan syndrome and Costello syndrome. Among patients with CFC syndrome, 23% (5/22) have autism/autistic features	Cardio-facio-cutaneous syndrome	115150	Cardiofaciocutaneous syndrome	AD	3	7
CHD7	55636	chromodomain helicase DNA binding protein 7	8q12.2	CHARGE syndrome (coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies); 68% (17/25) have ASD/autistic traits	CHARGE syndrome	214800	CHARGE syndrome	AD	3	8
VPS13B	157680	vacuolar protein sorting 13 homolog B (yeast)	8q22.2	Cohen syndrome (ID, microcephaly, facial dysmorphism, obesity, retinal dystrophy, and neutropenia); 49% (22/45) meet criteria for autism	Cohen syndrome	216550	Cohen syndrome	AR	3	8
EHMT1	79813	euchromatic histone-lysine N-methyltransferase 1	9q34.3	EHMT1 is responsible for the core phenotype of the 9q subtelomeric deletion syndrome (Kleefstra syndrome). 23% (5/22) of subjects with Kleefstra syndrome due to deletions or mutations have ASD/autistic features	9q subtelomeric deletion syndrome (Kleefstra syndrome)	610253	Kleefstra syndrome	AD	3	9
AP1S2	8905	adaptor-related protein complex 1, sigma 2 subunit	Xp22.2	X-linked ID and autism syndrome characterized by hypotonia, speech delay, aggressive behavior, and brain calcifications	X-linked mental retardation syndrome	300630	Mental retardation, X-linked 59	XL	2	X
PHF8	23133	PHD finger protein 8	Xp11.22	Siderius-Hamel syndrome (ID with cleft lip or cleft palate)	Siderius-Hamel syndrome (ID with cleft lip or cleft palate)	300263	Mental retardation syndrome, X-linked, Siderius type	XL	2	X
KIAA2022	340533	KIAA2022	Xq13.3	X-linked ID, progressive quadriparesia, and autism	X-linked ID	300524	Mental retardation, nonsyndromic, X-linked	XL	2	X
FGFR2	2263	fibroblast growth factor receptor 2	10q26	Apert syndrome	Apert syndrome	101200	Apert syndrome	AD	1	10
HRAS	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog	11p15.5	Costello syndrome	Costello syndrome	218040	Costello syndrome	AD	1	11
L2HGDH	79944	L-2-hydroxyglutarate dehydrogenase	14q21.3	l-2-hydroxyglutaric aciduria	L-2-hydroxyglutaric aciduria	236792	L-2-hydroxyglutaric aciduria	AR	1	14
GATM	2628	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	15q21.1	Arginine:glycine amidinotransferase (AGAT) deficiency (brain creatine deficiency, synthesis defect) has been described in only three families with 6 affected; autistic features were reported in one	glycine amidinotransferase (AGAT) deficiency	612718	AGAT deficiency	AR	1	15
GUCY2D	3000	guanylate cyclase 2D, membrane (retina-specific)	17p13.1	Leber congenital amaurosis	Leber congenital amaurosis	204000	Leber congenital amaurosis 1	AR	1	17
OTC	5009	ornithine carbamoyltransferase	Xp21.1	Ornithine transcarbamylase deficiency	Ornithine transcarbamylase deficiency	311250	Ornithine transcarbamylase deficiency	XL	1	X
CASK	8573	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	Xp11.4	Variable phenotypes, ranging from non-syndromic mild ID to severe ID with microcephaly, brain malformations, congenital nystagmus and dysmorphic facial features	X-linked mental retardation (XLMR) with microcephaly, optic atrophy and brainstem and cerebellar hypoplasia	300749	Mental retardation and microcephaly with pontine and cerebellar hypoplasia	XL	1	X
ZNF674	641339	zinc finger protein 674	Xp11.3	Non-syndromic X-linked ID	X-linked mental retardation	300851	Mental retardation, X-linked 92	XL	1	X
SYN1	6853	synapsin I	Xp11.23	X-linked epilepsy with variable learning disabilities and behavior disorders	epilepsy, learning difficulties, macrocephaly, and aggressive behaviour	300491	Epilepsy, X-linked, with variable learning disabilities and behavior disorders	XL	1	X
ZNF81	347344	zinc finger protein 81	Xp11.23	Non-syndromic X-linked ID	X-linked mental retardation	300498	Mental retardation, X-linked 45	XL	1	X
JARID1C	8242	lysine (K)-specific demethylase 5C	Xp11.22-p11.21	Large spectrum of phenotypes including ID with microcephaly, spasticity, short stature, epilepsy, and facial anomalies, as well as non-syndromic ID	non-syndromic ID	300534	Mental retardation, X-linked, syndromic, JARID1C-related	XL	1	X
SMC1A	8243	structural maintenance of chromosomes 1A	Xp11.22-p11.21	Cornelia de Lange syndrome (see NIPBL above, 5p13.2)	Cornelia de Lange syndrome	300590	Cornelia de Lange syndrome 2	XL	1	X
LAMP2	3920	lysosomal-associated membrane protein 2	Xq24	Danon disease (X-linked vacuolar cardiomyopathy and myopathy) is a lysosomal glycogen storage disorder	Danon disease	300257	Danon disease	XL	1	X
PHF6	84295	PHD finger protein 6	Xq26.3	Borjeson-Forssman-Lehmann syndrome (ID, epilepsy, and hypogonadism)	Borjeson-Forssman-Lehmann syndrome	301900	Borjeson-Forssman-Lehmann syndrome	XL	1	X
NPHP1	4867	nephronophthisis 1 (juvenile)	2q13	Joubert syndrome 4 and nephronophthisis (see AHI1 below, 6q23.3)	Joubert syndrome 4	609583	Joubert syndrome 4	AR	1	2
BTD	686	biotinidase	3p25	Biotinidase deficiency	Biotinidase deficiency	253260	Biotinidase deficiency	AR	1	3
PRSS12	8492	protease, serine, 12 (neurotrypsin, motopsin)	4q28.1	Autosomal recessive non-syndromic ID; mutated in 3 consanguineous families from North Africa, including one with two brothers with autism and ID	Autosomal recessive non-syndromic ID	249500	Mental retardation, autosomal recessive 1	AR	1	4
POMT1	10585	protein-O-mannosyltransferase 1	9q34.1	Limb-girdle muscular dystrophy with ID; Walker-Warburg syndrome	Walker-Warburg syndrome	609308	Muscular dystrophy-dystroglycanopathy (limb-girdle), type C, 1 	AR	1	9