AutismKB

Syndromic Autism Gene List (Chromosome View)

Some autism cases are observed in the context of a recognized syndrome (e.g., the fragile X syndrome) with known causal genes. These 99 genes were classified as syndromic autism genes in AutismKB.
This dataset comes from Catalina Betancur's review published in Brain Research in 2011(Betancur, 2011)

Refrence:
Betancur, C. (2011). Etiological heterogeneity in autism spectrum disorders: more than 100 genetic and genomic disorders and still counting. Brain Res 1380, 42-77.

Abbreviations: AD, autosomal dominant; AR, autosomal recessive; ASD, autism spectrum disorder; ID, intellectual disability; XL, X linked.
Gene_ID Gene_Symbol Band Gene Name Inheritance Disorder OMIM Detail
AutG4784 NFIX 19p13.3 nuclear factor I/X (CCAAT-binding transcription factor) AD Sotos-like overgrowth syndromeSotos syndrome (117550)
  • Description: Sotos-like overgrowth syndrome with advanced bone age, macrocephaly, ID, scoliosis, and unusual facial features.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20673863;
AutG1760 DMPK 19q13.3 dystrophia myotonica-protein kinase AD Myotonic dystrophy 1 (Steinert disease)Myotonic dystrophy 1 (160900)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 8810716; 18228241; 9183272; 2789860;
AutG6899 TBX1 22q11.21 T-box 1 AD 22q11 deletion syndrome phenotypeVelocardiofacial syndrome (192430)
  • Description: 22q11 deletion syndrome phenotype (velocardiofacial/DiGeorge syndrome);22% (9/41) patients with velocardiofacial syndrome also have ASD.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 16684884; 17937445;
AutG85358 SHANK3 22q13.3 SH3 and multiple ankyrin repeat domains 3 AD 22q13 deletion syndromeChromosome 22q13.3 deletion syndrome (606232)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20186804; 17173049; 18615476; 19736351; 15286229; 17999366; 10735630;
AutG55777 MBD5 2q23.1 methyl-CpG binding domain protein 5 AD 2q23.1 microdeletion syndromeMental retardation (156200)
  • Description: MBD5 is the only gene deleted in all subjects with the 2q23.1 microdeletion syndrome.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 18812405; 19809484;
AutG6323 SCN1A 2q24.3 sodium channel, voltage-gated, type I, alpha subunit AD Dravet syndromeDravet syndrome (607208)
  • Description: Severe myoclonic epilepsy of infancy (Dravet syndrome); ASD or autistic features have been reported repeatedly.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 16893627; -; 16122630; 16122630; 17030758; 19400878; 19764027; 21620773;
AutG23314 SATB2 2q33 SATB homeobox 2 AD 2q33.1 microdeletion syndromeCleft palate and mental retardation (119540)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 18252227; 16179223;
AutG27086 FOXP1 3p14.1 forkhead box P1 AD sporadic nonsyndromic IDMental retardation with language impairment and autistic features (613670)
  • Description: Autosomal dominant non-syndromic ID and ASD; disrupted in two patients with ID and autism/ASD.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20950788;
AutG25836 NIPBL 5p13.2 Nipped-B homolog (Drosophila) AD Cornelia de Lange SyndromeCornelia de Lange syndrome 1 (122470)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 17845236; 10490439; 16236812; 18564888; 19043149;
AutG4208 MEF2C 5q14 myocyte enhancer factor 2C AD 5q14.3 microdeletion syndromeChromosome 5q14.3 deletion syndrome (613443)
  • Description: MEF2C is responsible for the 5q14.3 microdeletion syndrome; both mutations and deletions have been described in individuals with ASD or autistic behavior.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20729728; 20412115; 20333642; 20513142;
AutG64324 NSD1 5q35 nuclear receptor binding SET domain protein 1 AD Sotos syndromeSotos syndrome (117550)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 16419094; 15318025; 15070547; 10766977; 2347353; 11942428; 16980810; 2055890; 18001468; 2347353;
AutG673 BRAF 7q34 v-raf murine sarcoma viral oncogene homolog B1 AD Cardio-facio-cutaneous syndromeCardiofaciocutaneous syndrome (115150)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 19953625; 17704260; 18456719; 18039235;
AutG55636 CHD7 8q12.2 chromodomain helicase DNA binding protein 7 AD CHARGE syndromeCHARGE syndrome (214800)
  • Description: CHARGE syndrome (coloboma, heart anomaly, choanal atresia, retardation, genital and ear anomalies); 68% (17/25) have ASD/autistic traits.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 15637726; 16359593; 15688419; 19709852; 19664354; 15633180;
AutG79813 EHMT1 9q34.3 euchromatic histone-lysine N-methyltransferase 1 AD 9q subtelomeric deletion syndrome (Kleefstra syndrome)Kleefstra syndrome (610253)
  • Description: 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.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 11840483; 12515261; 15054842; 15805155; 19264732; -;
AutG9378 NRXN1 2p16.3 neurexin 1 AD?/AR (Pitt-Hopkins-like) Pitt-Hopkins-like mental retardationPitt-Hopkins-like syndrome 2 (600565)
  • Description: Disrupted in ASD, ID, and other neurodevelopmental and psychiatric disorders (autosomal dominant?); Pitt-Hopkins-like syndrome-2 (autosomal recessive).
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20468056; 19404257; 19736351; 18179900; 20531469; 17322880; 20162629; 19896112;
AutG80184 CEP290 12q21.32 centrosomal protein 290kDa AR Joubert syndrome 5Joubert syndrome 5 (610188)
  • Description: Joubert syndrome 5; Leber congenital amaurosis (see AHI1 above, 6q23.3).
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 20683928; 17345604; 17409309;
AutG5053 PAH 12q22-q24.2 phenylalanine hydroxylase AR PhenylketonuriaPhenylketonuria (261600)
  • Description: Phenylketonuria was identified as a cause of ASD in older studies, but it is no longer observed where neonatal testing exists.
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 12757360; 17607414; 11897827; 1391074; 2597924;
AutG23322 RPGRIP1L 16q12.2 RPGRIP1-like AR COACH syndromeCOACH syndrome (216360)
  • Description: Joubert syndrome 7, Meckel syndrome, COACH syndrome (Joubert syndrome with congenital hepatic fibrosis).
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 19574260;
AutG6448 SGSH 17q25.3 N-sulfoglucosamine sulfohydrolase AR Sanfilippo syndrome AMucopolysaccharidisis type IIIA (Sanfilippo A) (252900)
  • Description: Sanfilippo syndrome A (mucopolysaccharidosis III A).
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 8879465; 2244638; 11202024;
AutG2593 GAMT 19p13.3 guanidinoacetate N-methyltransferase AR Guanidine acetate methyltransferase (GAMT) deficiencyGAMT deficiency (612736)
  • Description: Guanidine acetate methyltransferase (GAMT) deficiency (brain creatine deficiency, synthesis defect).
  • Evidence Level: Level 3: The gene has been reported in more than one family with ASD/autistic features, but the disorder hasn't been a generally acknowledged ASD related disorder.
  • Reference(s): 19892372; 20301745; 17336114;
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Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

  • Studies: 616
  • Genes: 3,075
  • SNPs/VNTRs: 3,386
  • CNVs: 4,617
  • Linkage Regions: 158
  • Last Update: 05/25/2012
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