Table 1 Array results of patients with ASD having pathogenic and likely pathogenic CNVs. Genomic coordinates were listed in human assembly GRCh37/hg19. Genes in bold represent the OMIM genes. Data set is available from the ArrayExpress repository, accession numbers E-MTAB-5672 and E-MTAB-5665

1

A0572B

M/4 years

arr[GRCh37] 7q31.1(110978196_111337169)x1

0.36 Mb deletion

IMMP2L

VUS

Paternally inherited

High-functioning ASD

arr[GRCh37] 15q25.2q26.1(84642246_91626219)x1

6.98 Mb deletion

ADAMTSL3, UBE2Q2L, GOLGA6L4, ZSCAN2, WDR73, NMB, SEC11A, ZNF592, ALPK3, SLC28A1, PDE8A, GOLGA6L3, AKAP13, KLHL25, AGBL1, NTRK3, MRPL46, MRPS11, DET1, AEN, ISG20, ACAN, HAPLN3, MFGE8, ABHD2, RLBP1, FANCI, POLG, RHCG, TICRR, KIF7, PLIN1, PEX11A, WDR93, MESP1, MESP2, ANPEP, C15orf38, AP3S2, ARPIN, ZNF710, IDH2, SEMA4B, CIB1, GDPGP1, NGRN, ZNF774, IQGAP1, CRTC3, BLM, FURIN, FES, MAN2A2, UNC45A, HDDC3, RCCD1, PRC1, VPS33B

Pathogenic

De novo

2

AGG0013

M/18 months

arr[GRCh37] 16p11.2(28488491_29046284)x1

0.56 Mb deletion

CLN3, APOBR, IL27, NUPR1, SGF29, SULT1A2, SULT1A1, NPIPB8, EIF3C, EIF3CL, NPIP89, ATXN2L, TUFM, SH2B1, ATP2A1, RABEP2, CD19, NFATC21P, SPNS1, LAT

Pathogenic

De novo

GDD, ASD

3

AGG0207

F/32 months

arr[GRCh37] Xp22.33(296519_4021220)x1

3.72 Mb deletion

PPP2R3B, SHOX, CRLF2, CSF2RA, IL3RA, SLC25A6, ASMTL, P2RY8, AKAP17A, ASMT, DHRSX, ZBED1, CD99, XG, GYG2, ARSD, ARSE, ARSH, ARSF, MXRA5, PRKX

Pathogenic

Not maternally inherited

Short stature, GDD, ASD

4

AGG0238

M/29 months

arr(X)x2,(Y)x1

XXY

(Klinefelter syndrome)

Pathogenic

De novo

Developmental language delay, ASD with ADHD features

5

AGG0318

F/26 months

arr[GRCh37] 1q44(246807340_249208105)x1

2.40 Mb deletion

CNST, SCCPDH, AHCTF1, ZNF695, ZNF670, ZNF669, C1orf229, ZNF124, VN1R5, ZNF496, NLRP3, GCSAML, TRIM58, LYPD8, SH3BP5L, ZNF672, ZNF692, PGBD2

Pathogenic

Inheritance not known; unbalanced translocation t(1;8)

ASD

arr[GRCh37] 8q24.22q24.3(135567463_146304022)x3

10.76 Mb duplication

ZFAT, KHDRBS3, FAM135B, COL22A1, KCNK9, TRAPPC9, CHRAC1, AGO2, PTK2, DENND3, SLC45A4, GPR20, PTP4A3, MROH5, TSNARE1, ADGRB1, ARC, JRK, PSCA, LY6K, THEM6, SLURP1, LYPD2, LYNX1, LY6D, GML, CYP11B1, CYP11B2, LY6E, C8orf31, LY6H, GPIHBP1, ZFP41, GLI4, ZNF696, TOP1MT, RHPN1, MAFA, ZC3H3, GSDMD, MROH6, NAPRT, EEF1D, TIGD5, PYCRL, TSTA3, ZNF623, ZNF707, CCDC166, MAPK15, FAM83H, SCRIB, PUF60, NRBP2, EPPK1, PLEC, PARP10, GRINA, SPATC1, OPLAH, EXOSC4, GPAA1, CYC1, SHARPIN, MAF1, WDR97, HGH1, BOP1, SCX, HSF1, DGAT1, SCRT1, TMEM249, FBXL6, SLC52A2, ADCK5, CPSF1, SLC39A4, VPS28, TONSL, CYHR1, KIFC2, FOXH1, PPP1R16A, GPT, MFSD3, RECQL4, LRRC14, LRRC24, C8orf82, ARHGAP39, ZNF251, ZNF34, RPL8, ZNF517, ZNF7, COMMD5, ZNF250, ZNF16, C8orf33

Pathogenic

6

AGG0126

M/29 months

arr[GRCh37] 6q26(162621987_163095834)x3

0.47 Mb duplication

PARK2

likely pathogenic

De novo

Speech delay; ASD; Hypospadias

7

AGG0128

M/23 months

arr[GRCh37] 16p13.11(15125758_16287903)x3

1.16 Mb duplication

PDXDC1, NTAN1, RRN3, MPV17L, C16orf45, KIAA0430, NDE1, MYH11, FOPNL, ABCC1, ABCC6

Pathogenic

Maternally inherited

ASD

8

AGG0228

M/17 years

arr[GRCh37] 16p13.11(15125758_16287903)x3

1.16 Mb duplication

PDXDC1, NTAN1, RRN3, MPV17L, C16orf45, KIAA0430, NDE1, MYH11, FOPNL, ABCC1, ABCC6

Pathogenic

Inheritance not known

Epilepsy; GDD; ASD

9

AGG0437

M/29 months

arr[GRCh37] 11p11.2(48103669_48388756)x2~3

0.29 Mb duplication (mosaic)

PTPRJ, OR4B1, OR4X2, OR4ZX1, OR4S1, OR4C3, OR4C45

Pathogenic

Inheritance not known

ASD

arr[GRCh37] 11q12.1q12.2(55896790_61443324)x2~3

5.55 Mb duplication (mosaic)

LRRC55, APLNR, TNKS1BP1, SSRP1, P2RX3, PRG3, PRG2, SLC43A3, RTN4RL2, SLC43A1, TIMM10, SMTNL1, UBE2L6, SERPING1, TPEL4, CLP1, ZDHHC5, MED19, TMX2 . C11orf31, BTBD18, CTNND1, LPXN, ZFP91, CNTF, GLYAT, GLYATL2, AK294973, GLYALT1, FAM111B, FAM111A, DTX4, MPEG1, OSBP, PATL1, STX3, MRPL16, GIF, TCN1, AB231702, PLAC1L, CCDC86, PTGDR2, ZP1 , PRPF19, TMEM109, TMEM132A, SLC15A3, CD6, VPS37C, PGA3, PGA4, PGA5, VWCE, DDB1, TKFC, CYB561A3, TMEM138, TMEM216, CPSF7, SDHAF2, PPP1R32, LRRC10B, ZYT7

Pathogenic

Inheritance not known