Table 2.

Genes and loci disrupted by BCAs and likely associated with developmental disorders

Pathogenic
Genomic imbalances at breakpoints	2q24.3 deletion (SCN9A); 4q34 deletion; 6q13-q14.1 deletion (PHIP)a; 6q14.1 deletion (TBX18)b; 6q22.1–22.31 deletion (GJA1); 10p15.3-p14 deletion (GATA3); 11p14.2 deletion; 12p12.1-p11.22 deletion (SOX5, PTHLH); 13q14.2 deletion; 14q12-q21.1 deletion (NFKBIA, NKX2-1)c; 18p11.32-p11.22 deletiond; 19q12-q13.11 deletion; Xq25 duplication
Gene disruption	AHDC1; AUTS2(x2); CAMTA1; CDKL5; CHD7; CHD8; CTNND2; CUL3; DYRK1A; EFTUD2; EHMT1; FGFR1; FOXP1; FOXP2; GRIN2B; IL1RAPL1; KAT6B; KDM6A(x2); MBD5(x3); MEF2C; MTAP; MYT1L(x2); MYO6e; NALCN; NFIA; NFIX; NODAL; NOTCH2; NR2F1; NR5A1; NRXN1; NSD1; PAK3; PDE10A; PHF21A(x2)d; PHIPe; SATB2; SCN1A; SMS; SNRPN-SNURF(x3); SOX5(x2); SPAST; TCF12; TCF4; WAC; ZBTB20(x2)
Likely Pathogenic
Genomic imbalances at breakpoints	2p21-p13.3 duplication (NRXN1)
Gene disruption	ARIH1; BBX; CACNA2D3; CACNA1C; CADPS2f CDK6(x2); CELSR1; EP400g; GNB1; GRM1h; KCND2; MDN1; NFIB; NPAS3(x4)c,i; NRXN3; PRPF40A; PSD3j; PTPRZ1(x3)a,f; ROBO2; SHROOM4g; SPTBN1; SYNCRIP(x2)b,j; STXBP5h; UPF2; 11p15 region
Positional effect	FOXG1(x4)i; MEF2C(x7); PITX2; SATB2(x3)j; SLC2A1; SOX9; SRCAP

Details on BCA interpretation are provided in Methods and Supplementary Table 7. Genes that have been associated to dominant developmental disorders and encompassed by genomic imbalances at breakpoints are indicated in brackets; lower-scripts indicate when a gene was disrupted by a BCA in multiple subjects; upper-scripts report subjects with a BCA disrupting multiple genes/loci that may each contribute to their developmental phenotype and to distinct clinical features;

^a: Subject DGAP133;

^b: Subject DGAP317,

^c: subject DGAP002,

^d: subject DGAP316,

^e: subject NIJ2,

^f: subject DGAP168,

^g: subject DGAP172,

^h: DGPA196;

ⁱ: DGAP246;

^j: DGAP237.