Table 1.
Disorder-related SNVs/indels.
| Gene | Funca | NT_AAChangeb | Inheritancec | clinical significanced | sampleID | GeneSetse |
|---|---|---|---|---|---|---|
| ARID1B† | SG | NM_020732:c.C2692T:p.R898* | DN | P | BK-303–03 | SFARI(1)|DD93|BC253|ID526|MG237 |
| ARID1B† | 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.2682–2A>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† | MIS | NM_001159676:c.T629C:p.F210S | DN | PDR | BK-611–01 | BC253|ID_C628 |
| SYNCRIP† | 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† | MIS | NM_015567:c.G175T:p.G59C | DN | PDR | BK-354–03 | SFARI|MG237 |
| SLITRK5† | 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† | MIS | NM_014831:c.G2701A:p.V901I | DN | PDR | BK-358–03 | - |
| TRANK1† | 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 |
a.
SG, stop-gain; FS, frameshift; SP, splicing site; MIS, missense; NFS, nonframeshift.
b.
Canonical isoform presented.
c.
DN, de novo; PI, paternal inheritance; MI, maternal inheritance.
d.
P, pathogenic; LP, likely pathogenic; PDR, potentially disorder-related variants beyond the clinically relevant P and LP variants.
e.
List of 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. Nat Genet 2018; MG237, 237 NDD genes with nominal significance for enrichment or clustering of missense de novo variants from Geisheker al. Nat Neurosci 2017; ID526, ID_C628, 526 ID genes and 628 candidate ID genes curated by Gilissen et al. Nature 2014 (also see Supplementary Methods for details and corresponding reference).
†
Recurrent variant identified.