Table 1 Disorder-related single-nucleotide variants (SNVs)/indels

From: Genome sequencing identifies multiple deleterious variants in autism patients with more severe phenotypes

Gene

Funca

NT_AAChangeb

Inheritancec

Clinical significanced

Sample ID

Gene setse

ARID1B f

SG

NM_020732:c.C2692T:p.R898*

DN

P

BK-303-03

SFARI(1)|DD93|BC253|ID526|MG237

ARID1B f

SG

NM_020732:c.C2536T:p.Q846*

DN

P

BK-418-03

SFARI(1)|DD93|BC253|ID526|MG237

MED13L

SG

NM_015335:c.G4076A:p.W1359*

DN

P

BK-242-03

SFARI(2)|DD93|BC253|ID_C628

WDFY3

SG

NM_014991:c.A2932T:p.R978*

DN

P

BK-283-03

SFARI(2)|BC253|ID_C628

RERE

SG

NM_001042681:c.C2278T:p.Q760*

DN

P

BK-186-03

SFARI(4)

ADNP

FS

NM_001282532:c.2250_2274del:p.V751Mfs*13

DN

P

BK-246-05

SFARI(1)|BC253|ID_C628

CIC

FS

NM_001304815:c.884_893del:p.A295Pfs*26

DN

P

BK-521-03

SFARI(2)

OPHN1

FS

NM_002547:c.932_933insCA:p.Q311Hfs*7

DN

P

BK-359-03

SFARI(3)|ID526

CHD8

SP

NM_020920:c.2682-2 A > G

DN

P

BK-186-03

SFARI(1)|DD93|BC253|MG237

FOXP1

SP

NM_001244815:c.1728 + 1- > TGCAGCTTTACAG

DN

P

BK-248-03

SFARI(2)|DD93|BC253|ID526|MG237

ASXL1

SG

NM_015338:c.C1045T:p.Q349*

MI

P

BK-483-03

DD93|ID526

GNB1

MIS

NM_001282539:c.G229A:p.G77S

DN

P

BK-328-03

-

MEF2C

MIS

NM_001193348:c.C43T:p.R15C

DN

P

BK-192-03

SFARI(4)|DD93|BC253|ID526|MG237

KMT5B

MIS

NM_016028:c.G791C:p.W264S

DN

P

BK-255-03

SFARI(1)|DD93|BC253|ID526

NR4A2

FS

NM_006186:c.601_602insGTCC:p.P201Rfs*82

DN

LP

BK-370-03

BC253|ID526|MG237

SMC3

MIS

NM_005445:c.C2413T:p.R805C

DN

LP

BK-255-03

SFARI(4)|BC253|MG237|ID_C628

STXBP1

MIS

NM_001032221:c.C560T:p.P187L

DN

LP

BK-277-03

SFARI(3)|DD93|BC253|ID526|MG237

GRIA1

MIS

NM_001258021:c.G2264A:p.G755D

DN

LP

BK-401-03

SFARI(2)|MG237 |ID_C628

KAT6A

MIS

NM_001305878:c.C1582T:p.P528S

DN

LP

BK-523-03

SFARI(3)|DD93|BC253

SATB2

MIS

NM_001172509:c.A1861T:p.I621F

DN

LP

BK-550-03

SFARI(4)|DD93|BC253|ID526|MG237

POGZ

MIS

NM_015100:c.G3048T:p.E1016D

DN

LP

BK-219-03

SFARI(1)|DD93|BC253|MG237|ID_C628

DYNC1H1

MIS

NM_001376:c.A13088C:p.K4363T

DN

LP

BK-283-03

SFARI(3)|DD93|BC253|ID526

SYNCRIP f

MIS

NM_001159676:c.T629C:p.F210S

DN

PDR

BK-611-01

BC253|ID_C628

SYNCRIP f

MIS

NM_001159676:c.1573_1574CA_TT:p.Q525L

DN

PDR

BK-252-03

BC253|ID_C628

JMJD1C

FS

NM_032776:c.667_668insA:p.M223Nfs*3

DN

PDR

BK-418-03

SFARI(4)

THBS1

SG

NM_003246:c.C2875T:p.R959*

DN

PDR

BK-396-04

SFARI|ID_C628

LARP4B

FS

NM_015155:c.801_802del:p.C267*

DN

PDR

BK-205-03

BC253

MCM3AP

FS

NM_003906:c.276delC:p.F93Lfs*42

DN

PDR

BK-302-03

ID_C628

KIRREL3

MIS

NM_032531:c.G1985A:p.R662H

DN

PDR

BK-330-03

SFARI(3)|ID526

RPS6KA2

MIS

NM_001006932:c.G1720A:p.G574R

DN

PDR

BK-222-03

SFARI(4)

TUB

MIS

NM_003320:c.G139A:p.G47S

DN

PDR

BK-141-03

MG237

DMXL2

MIS

NM_001174116:c.C6137T:p.A2046V

DN

PDR

BK-175-03

SFARI(4)

TOP1

MIS

NM_003286:c.A1217T:p.H406L

DN

PDR

BK-254-03

SFARI(5)|ID_C628

SLC9A3

MIS

NM_001284351:c.C914T:p.S305L

DN

PDR

BK-523-03

MG237

KCNK9

MIS

NM_001282534:c.C907T:p.R303C

DN

PDR

BK-227-03

ID_C628

SPG11

MIS

NM_001160227:c.C4955G:p.T1652R

DN

PDR

BK-599-07

MG237

SLITRK5 f

MIS

NM_015567:c.G175T:p.G59C

DN

PDR

BK-354-03

SFARI|MG237

SLITRK5 f

MIS

NM_015567:c.C976T:p.P326S

DN

PDR

BK-372-03

SFARI|MG237

CLSTN3

MIS

NM_014718:c.T599C:p.I200T

DN

PDR

BK-187-04

SFARI(5)

SMG9

MIS

NM_019108:c.A947G:p.H316R

DN

PDR

BK-198-03

ID_C628

MYT1

MIS

NM_004535:c.C2138T:p.S713F

DN

PDR

BK-516-03

ID_C628

ACACB

MIS

NM_001093:c.A1963G:p.S655G

DN

PDR

BK-162-03

ID_C628

GRM5

MIS

NM_001143831:c.A523G:p.T175A

DN

PDR

BK-307-03

SFARI|ID_C628

CSMD1

MIS

NM_033225:c.A2381C:p.H794P

DN

PDR

BK-146-03

SFARI

SDK1

MIS

NM_152744:c.G6016A:p.E2006K

DN

PDR

BK-401-03

SFARI

TRANK1 f

MIS

NM_014831:c.G2701A:p.V901I

DN

PDR

BK-358-03

-

TRANK1 f

MIS

NM_014831:c.C6326A:p.T2109K

DN

PDR

BK-413-03

-

RRP8

MIS

NM_015324:c.G803A:p.R268H

DN

PDR

BK-590-01

BC253

UPF2

MIS

NM_080599:c.G91T:p.V31L

DN

PDR

BK-328-03

SFARI(5)|ID_C628

PTPRT

MIS

NM_007050:c.G548A:p.R183Q

DN

PDR

BK-261-04

SFARI|ID_C628

KCNS3

MIS

NM_001282428:c.G601A:p.A201T

DN

PDR

BK-144-03

BC253

PAFAH1B3

MIS

NM_001145939:c.T571C:p.Y191H

DN

PDR

BK-460-03

ID_C628

NALCN

MIS

NM_052867:c.C682T:p.H228Y

DN

PDR

BK-428-03

ID_C628

BIRC6

MIS

NM_016252:c.A3931G:p.I1311V

DN

PDR

BK-280-03

SFARI|ID_C628

STARD9

MIS

NM_020759:c.G4802A:p.R1601Q

DN

PDR

BK-473-03

BC253

FASN

MIS

NM_004104:c.G2719A:p.V907I

DN

PDR

BK-135-03

ID_C628

DST

NFS

NM_001144769:c.97_98insCCACCATCG:p.V33delinsATIV

DN

PDR

BK-522-03

SFARI(4)|ID_C628

TNRC6B

SP

NM_001024843:c.46-2A>G

PI

PDR

BK-182-03

SFARI(2)

DLG4

SP

NM_001365:c.20-1G>C

MI

PDR

BK-201-03

SFARI|Coe124|ID_C628

LAMB1

FS

NM_002291:c.144delG:p.K49Sfs*4

PI

PDR

BK-445-03

SFARI(3)

ATP10A

SG

NM_024490:c.C2397A:p.Y799*

MI

PDR

BK-254-03

SFARI(3)

ELP4

FS

NM_001288725:c.284delC:p.S95Yfs*64

PI

PDR

BK-219-03

SFARI(3)

LZTR1

FS

NM_006767:c.772delT:p.F258Lfs*93

MI

PDR

BK-384-03

SFARI(3)|ID_C628

  1. aFS frameshift, NFS nonframeshift, SG stop-gain, SP splicing site.
  2. bCanonical isoform presented.
  3. cDN de novo, MI maternal inheritance, PI paternal inheritance.
  4. dLP likely pathogenic, P pathogenic, PDR potentially disorder-related variants beyond the clinically relevant P and LP variants.
  5. eList of neurodevelopmental disorder (NDD) gene sets that the genes belong to. SFARI, 970 ASD-associated genes from SFARI gene database; DD93, 93 developmental delay genes identified from DDD study 2017; BC253, 253 significant NDD genes from Coe et al.;5 MG237, 237 NDD genes with nominal significance for enrichment or clustering of missense de novo variants from Geisheker et al.;41 ID526, ID_C628, 526 intellectual disability (ID) genes and 628 candidate ID genes curated by Gilissen et al.42 (also see Supplementary Methods for details and corresponding references).
  6. fRecurrent variant identified.
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