Table 2

Single nucleotide variants in scaffolding genes associated with schizophrenia, autism-spectrum disorders and other clinical phenotypes of interest

Gene	Single nucleotide variants				Sources

	Schizophrenia	Autism-spectrum disorders	Schizophrenia and autism-spectrum disorders	Other associated phenotypes
DLG1	g.196863463C>T49 g.196812562A>T, g.196812614A>T, g.196842947T>C, g.196867096C>A50 g.196863502G>C^*127	g.196817764T>C59	—	—	Fromer et al.49 Purcell et al.50 Iossifov et al.59 Xing et al.127
DLG2	g.83194295C>T49 g.83180351C>T, g.83180371T>G, g.83243821T>G, g.83497759G>A50	—	—	—	Fromer et al.49 Purcell et al.50
DLG4	g.7096826C>T50	g.7106562G>Aa127	—	—	Purcell et al.50 Xing et al.127
DLGAP1	c.1922A>G114	—	—	—	Li et al.114
DLGAP2	g.1497520G>A50 c.−69+9C>T, c.−69+13C>T, c.−69+47C>T, c.−69+55C>T, c.−32A>G, c.341A>G,^* c.438C>T, c.990+60T>C, c.1192G>A, c.1920+37A>G, c.1920+94T>A, c.1927G>A, c.2493G>C, c.2634C>T, c.2797G>A,^* c.2884G>A,^* c.2663G>A116	c.44C>T,^* c.277C>A,^* c.545G>A,^* c.574G>T, c.1516T>C,^* c.2392G>C,^* c.970A>T115 g.1616734C>T^*127 g.1626547G>C59	c.841C>G,^^† c.2135C>T,^†^‡ c.2750C>T^^†^‡115,116	—	Purcell et al.50 Iossifov et al.59 Chien et al.115 Li et al.116 Xing et al.127
DLGAP3	c.1141G>A, c.1759G>C, c.2309G>T, c.2578−11C>T128	35365700G>A59	—	—	Iossifov et al.59 Li et al.128
SHANK1	g.51205733T>A50	g.51220161C>T, g.51206952G>A,^* g.51205840C>T,^* g.51170826G>A, g.51170775G>A, g.51165632C>T129 g.51220076C>T, g.51219998C>T, g.51215287C>T,^* g.51206988G<T, g.51205886C>T,^* g.51191281C>T,^* g.51172180G>A, g.51171270C>T,^* g.51170856C>T, g.51170854C>T,^* g.51170779C>T, g.51170674C>A,^* g.51170418G>A, g.51170407G>T, g.51170362A>T,^* g.51170359T>C,^* g.51170046A>T,^* g.51169830C>T,^* g.51165932C>T, g.51165929C>T,^* g.51165767G>A,^* g.51165574C>A^*130	—	—	Purcell et al.50 Leblond et al.129 Sato et al.130
SHANK2	g.70666649G>A, g.70666499C>A, g.70544817G>T, g.70349029T>C, g.70333526G>T, g.70333043G>T, g.70333967G>A, g.70331576C>T, g.70331462G>T, g.70319333C>A131 g.70644595G>A^*132	c.76C>T, c.622C>T, c.3380C>T, c.4048G>A, c.467A>G, c.492C>T, c.527−18C>A, c.640+11C>T, c.80033C>T, c.942+19G>A, c.924+133G>C, c.1061−81C>T, c.1141+49G>A, c.1148−109C>T, c.1201A>C, c.1264G>A, c.1302+35G>A, c.1303−54C>T, g.70336411G>A,^* c.1392G>T, c.1923G>A, c.2052G>A, c.2823C>T, c.3135C>T, c.3843−12C>T, g.70666749G>A,^* g.70644566G>A,^* g.70331881G>A,^* g.70319339C>T133 g.70666635G>A,^* g.70544853C>A,^* g.70348949C>A,^* g.70348913C>T,^* g.70332914C>T,^* g.70332890C>T,^* g.70332272C>T,^* g.70331795C>T,^* g.70319359A>G^*134 g.70821018C>G g.70858273A>C59	—	c.76C>T, c.467A>G, c.942+19G>A, c.924+133G>C, c.1141+49G>A, c.1148−109C>T (associated with intellectual disability)133	Iossifov et al.59 Peykov et al.131 Homann et al.132 Berkel et al.133 Leblond et al.134
SHANK3	g.49484091C>T g.49506476C>T46,135 g.51117040G/A, g.51117200G/T, g.51117489C/T, g.51117580C/T, g.51117585G/A, g.51137217A/G, g.51143287C/T, g.51144513C/G, g.51153371G/A, g.51159735C/T, g.51159798A/G, g.51159802C/T, g.51159828G/A, g.51160154G/A, g.51169180A/G51	g.51117341C>G, g.51159953G>A, g.51169240A>G136 g.51159293G>T^129,136 c.670G>A136,138 g.51121780C>T,^ g.51159458G>T,^* g.51113103C>T136,140 g.51117094C>G,^* g.51160615G>T137 g.51142357C>T, g.51153464G>A,^* g.51158686G>T,^* g.51158945T>C,^* g.51159965C>A,^* g.51159988C>T,^* g.51160086A>T,^* g.51160057G>A129 c.1527G>A138 g.51113615T>C^139 g.51121844A>G,^ g.51123071C>T,^* g.51159169G>T,^* g.51160477C>G, g.51169213G>A,^* g.51160589T>C141 g.51159778G>A,^* g.51160049C>T,^* ^§ 141,142 c.1563G>A, c.1967G>A, c.4908C>T142 g.1159884G>A,^* g.51160018A>T, g.51169259C>T^* (p.1572A>V), 51169364C>T,^* 51169442G>A,^* 51169459C>T, 51169463C>T,^* 51169480G>A, g.51169207C>T^* g.51169499G>A143 c.612C>A, c.763C>T, c.898C>T, c.920C>G, c.1315C>T, c.1337G>T, c. 3761C>T, c.3764C>T, c.3836C>T, c.4025C>T, c.4405G>C, c.4406G>T, c.4490G>A, c.4720G>A144 c.5008A>T145	g.49506159G>T129,135,136	g.49506476C>T, c.5008A>T, c.1527G>A (associated with intellectual disability)46,138,145	Awadalla et al.46 Girard et al.51 Leblond et al.129 Gauthier et al.135 Durand et al.136 Boccuto et al.137 Soorya et al.138 Gauthier et al.139 Durand et al.140 Moessner et al.141 Waga et al.142 Schaaf et al.143 Kelleher et al.144 Cochoy et al.145
HOMER1	IVS4 þ146	c.195G>T, c.290C>T, c.425C>T, c.968G>A, c.1090C>T144			Kelleher et al.144 Norton et al.146

↵* These variants have functional impact on the protein using the PolyPhen-2 or the Pmunt computer program.
↵† Chien and colleagues also found this variant in controls.115
↵‡ Li and colleagues also found this variant in controls.116
↵§ Waga and colleagues also found this variant in controls.142