Table 2 Summary of findings from gene list comparison and list of most commonly listed genes

From: Heterogeneity in clinical sequencing tests marketed for autism spectrum disorders

Key findings
● Number of genes included on ASD gene sequencing panels ranged from 11 to 2562
● 2928 unique genes identified across 21 labs
● When comparing the gene lists of 21 labs (see Supplementary Table S1)
 ○ Only one gene (MECP2) was shared by all labs
 ○ 63 genes shared by at least 10/21 labs
 ○ Two sets of labs had the same gene lists
● Of the top 16 genes shared by 16 or more panels,
 ○ 12 were associated with known OMIM syndromesa primarily involving physical/systemic features, of which 3 (MECP2, PTEN, and CNTNAP2) included autism susceptibility
 ○ 4 (NLGN4X, PTCHD1, NLGN3, and FOXP1) were associated with primarily a neurocognitive presentation (ASD, intellectual disability) in OMIM
 ○ 2 (UBE3A and SHANK3) overlapped with known ASD-associated CNV regions
● The top 178 genes shared across 21 labs did NOT include 39 genes cited on 2 or more ASD gene listsc
Top shared genesb
Gene name Labs OMIM gene association (OMIM#) a
MECP2 c 21/21 Encephalopathy (300673); Mental retardation (300260)(300055); Rett syndrome (312750); Autism susceptibility (300496)
NLGN4X 20/21 Mental retardation (300495); Asperger syndrome susceptibility (300497); Autism susceptibility (300495)
CACNA1C c 19/21 Brugada syndrome 3 (611875); Timothy syndrome (601005)
NRXN1 c 19/21 Pitt-Hopkins-like syndrome 2 (614325); Schizophrenia susceptibility (614332)
PCDH19 19/21 Epileptic encephalopathy (300088)
PTCHD1 c 19/21 Autism susceptibility (300830)
UBE3A 19/21 Angelman syndrome (105830)
NLGN3 c 18/21 Asperger syndrome susceptibility (300494); Autism susceptibility (300425)
PTEN c 18/21 Bannayan-Riley-Ruvalcaba syndrome (153480); Cowden syndrome 1/ Lhermitte-Duclos syndrome (158350); Macrocephaly/autism syndrome (605309); VATER association with macrocephaly and ventriculomegaly (276950); Glioma susceptibility (613028); Meningioma (607174); Prostate cancer (176807)
SHANK3 c 18/21 Phelan-McDermid syndrome (606232); Schizophrenia (613950)
CDKL5 c 17/21 Epileptic encephalopathy (300672)
CNTNAP2 17/21 Cortical dysplasia-focal epilepsy syndrome/ Pitt-Hopkins like syndrome 1 (610042); Autism susceptibility (612100)
DHCR7 c 17/21 Smith-Lemli-Opitz syndrome (270400)
FOXP1 c 17/21 Mental retardation with language impairment and with or without autistic features (613670)
NSD1 c 17/21 Leukemia (601626); Sotos syndrome 1 (117550)
ARX c 16/21 Epileptic encephalopathy (308350); Hydranencephaly with abnormal genitalia (300215); Lissencephaly (300215); Mental retardation (300419); Partington syndrome (309510); Proud syndrome (300004)
  1. aOnline Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression. omim.org
  2. bList of the top 16 genes shared by 16 or more clinical ASD sequencing panels
  3. cGene listed on 2 or more of the following: SFARI list11 with gene score of 1 or 2; SPARK list12 as of April 2017; MSSNG list published in 2017;8 ASC list13 of genes with q value <0.3
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