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
AutG775 CACNA1C 12p13.3 calcium channel, voltage-dependent, L type, alpha 1C subunit AD Timothy syndromeTimothy syndrome (601005)
  • Description: 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.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 15454078; 20301577;
AutG7337 UBE3A 15q11.2 ubiquitin protein ligase E3A AD Angelman syndromeAngelman syndrome (105830)
  • Description: 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.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 17415598; 16183798; 15165432; 21831244;
AutG7249 TSC2 16p13.3 tuberous sclerosis 2 AD Tuberous sclerosisTuberous sclerosis-2 (191100)
  • Description: Tuberous sclerosis is caused by mutations in the TSC1 or TSC2 genes (see TSC1 above, 9q34.13).
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 9394941; 8132114; 14985384; 17936687; 16901420;
AutG7248 TSC1 9q34 tuberous sclerosis 1 AD Tuberous sclerosisTuberous sclerosis-1 (191100)
  • Description: 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%.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 9394941; 8132114; 14985384; 17936687; 16901420;
AutG1717 DHCR7 11q13.4 7-dehydrocholesterol reductase AR Smith-Lemli-Opitz syndromeSmith-Lemli-Opitz syndrome (270400)
  • Description: 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.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 16761297; 16874769; 11223857;
AutG26047 CNTNAP2 7q35 contactin associated protein-like 2 AR (AD too?) Cortical dysplasia-focal epilepsy syndromeCortical dysplasia-focal epilepsy syndrome (610042)
  • Description: 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.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 16571880; 20513142;
AutG2332 FMR1 Xq27.3 fragile X mental retardation 1 XL fragile X syndromeFragile X syndrome (300624)
  • Description: 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.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 17031449; 15070547; 20643379;
AutG4204 MECP2 Xq28 methyl CpG binding protein 2 (Rett syndrome) XL Rett syndromeRett syndrome (312750)
  • Description: MECP2 mutations or deletions cause Rett syndrome in females, and congenital encephalopathy or non-syndromic ID in males; MECP2 duplication syndrome, mostly in males.
  • Evidence Level: Level 4: The disorder is a generally acknowledged ASD related disorder.
  • Reference(s): 16418599; 12770674; 17286265; 12959422; 16980810; 12707946;
AutG5728 PTEN 10q23.3 phosphatase and tensin homolog AD PTEN hamartoma-tumor syndromePTEN hamartoma-tumor syndrome (601728)
  • Description: 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.
  • 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): 15805158; 17427195; 12920084; 11496368; 12567405; 19321504; 20533527; 18759867; 20814261; 17526801; 19265751;
AutG3481 IGF2 11p15.5 insulin-like growth factor 2 (somatomedin A) AD Beckwith-Wiedermann syndromeBeckwith-Wiedermann syndrome (130650)
  • Description: 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.
  • 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): 18314872;
AutG3845 KRAS 12p12.1 v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog AD Cardio-facio-cutaneous syndromeCardiofaciocutaneous syndrome (115150)
  • Description: Cardio-facio-cutaneous 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): 17704260; 18456719;
AutG5781 PTPN11 12q24 protein tyrosine phosphatase, non-receptor type 11 AD Noonan syndromeNoonan syndrome 1 (163950)
  • Description: Noonan syndrome (craniofacial anomalies, short stature, heart defects). In a sample of 65 children with Noonan syndrome, 8% had a diagnosis of 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): 8173225; 6662846; 19077116; 8725750;
AutG2290 FOXG1 14q13 forkhead box G1 AD Rett syndromeRett syndrome, congenital variant (613454)
  • Description: Deletions and mutations cause a congenital variant of Rett syndrome, duplications are associated with ID, severe speech delay, and epilepsy.
  • 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): 19029900; 19564653;
AutG5604 MAP2K1 15q22.1-q22.33 mitogen-activated protein kinase kinase 1 AD Cardio-facio-cutaneous syndromeCardiofaciocutaneous syndrome (115150)
  • Description: Cardio-facio-cutaneous 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): 17704260;
AutG1387 CREBBP 16p13.3 CREB binding protein AD Rubinstein-Taybi syndromeRubinstein-Taybi syndrome (180849)
  • Description: 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.
  • 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): 18792986; 19350377;
AutG5048 PAFAH1B1 17p13.3 platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa) AD Lissencephaly 1Lissencephaly 1 (607432)
  • Description: 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.
  • 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): 19136950; 20452996; 19667223;
AutG7531 YWHAE 17p13.3 tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptide AD Miller-Dieker syndromeMiller-Dieker lissencephaly syndrome (247200)
  • Description: 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.
  • 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): 19136950; 20452996;
AutG10743 RAI1 17p11.2 retinoic acid induced 1 AD Smith-Magenis syndromeSmith-Magenis syndrome (182290)
  • Description: Deletions or mutations of RAI1 cause Smith-Magenis syndrome; duplications result in Potocki-Lupski syndrome. ASDs are observed frequently in both syndromes.
  • 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): 18301319; 17334992; 9557889; 17357070; 16980810; 2425619; 3728561; 20110824; -; 8055249;
AutG84282 RNF135 17q11.2 ring finger protein 135 AD overgrowth IDOvergrowth syndrome (611358)
  • Description: 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.
  • 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): 17632510;
AutG4763 NF1 17q11.2 neurofibromin 1 AD Neurofibromatosis type 1Neurofibromatosis, type 1 (162200)
  • Description: 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).
  • 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): 9394941; 16980810; 17996402; 9932243;
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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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