Table 7.
Pathogenic or likely pathogenic CNVs found in the cohort
| CASE | CHD Phenotype |
Soft markers | Structural anomalies | CNV | Microarray Nomenclature | Size (Mbp) | Pathogenicity | Some of Relevant Genes | syndrome |
|---|---|---|---|---|---|---|---|---|---|
| #6 | VSD, | – | Facial dysmorphisms | del | arr[hg19] 3q29(194,654,896–197,363,564) × 1 | 2.71 | P | TFRC | Chromosome 3q29 microdeletion syndrome |
| #20 | TOF | – | Respiratory system | del | arr[hg19] 22q11.1q11.21(17,900,000–20,600,000) × 1 | 2.7 | P | ATP6V1E1, PEX26,TUBA8 | 22q11 deletion syndrome |
| #23 | PVS | – | – | del | arr[hg19] 2p25.3(50–450,000) × 1 | 0.45 | P | – | – |
| #24 | Complex CHD | – | – | dup | arr[hg19] 15q24.3q25.2(78,250,000–85,000,000) × 1 | 6.75 | P | ARNT2, RPS17,AP3B2 | Chromosome 15q25 deletion syndrome |
| #35 | Complex CHD | – | – | del | arr[hg19] 5p15.33p14.2(20,000–23,980,000) × 3 | 23.96 | P | SDHA, NDUFS6 | Mitochondrial complex II deficiency, Leigh syndrome(LS) |
| #35 | Complex CHD | – | – | dup | arr[hg19] 21(q22.12-q22.3)(37,780,000–48,100,000) × 3 | 10.32 | P | – | Down syndome |
| #39 | PAA | – | – | del | arr[hg19] 7q11.23(72,260,000–76,000,000) × 3 | 3.74 | P | POR |
7q11.23 duplication syndrome, WILLIAMS-BEUREN region duplication syndrome |
| #41 | d-TGA | – | – | dup | arr[hg19] 1p36.33p36.32(820,000–3,320,000) × 3 | 2.5 | LP | AGRN,B3GALT6, TMEM240 | congenital myasthenic syndrome-8 (CMS8), Ehlers-Danlos syndrome progeroid type 2 |
| #56 | DORV, PAA | – | – | del | arr[hg19] 5p15.33p15.1(20,000–16,500,000) × 1 | 16.48 | P | SDHA | 5p15 terminal (Cri du chat syndrome) region duplication,mitochondrial complex II deficiency[OMIM:252011] |
| #56 | DORV,PAA | – | – | dup | arr[hg19] 17q24.2q25.3(65,320,000–81,160,000)) × 3 | 15.84 | P | PSMD12 |
46 XX sex reversal 2, STANKIEWICZ-ISIDOR syndrome(STISS) |
| #59 | AVSD | – | – | del | arr[hg19] 20p12.3(6,300,001–8,580,000) × 3 | 2.28 | LP | BMP2 |
BRACHYDACTYLY, TYPE A2(BDA2), Early infantile epileptic encephalopathy-12 (EIEE12) |
| #78 | VSD + ASD | Single umbilical artery | Facial Dysmorphisms | del | arr[hg19] 7p22.3p22.1(40,000–6,740,000) × 1 | 6.7 | LP | BRAT1 | lethal neonatal rigidity and multifocal seizure syndrome |
| #78 | VSD + ASD | Single umbilical artery | Facial dysmorphisms | dup | arr[hg19] 12p13.33p13.31(160,000–8,320,000) × 3 | 8.16 | LP | CACNA1C, CCND2, CHD4 |
Timothy syndrome(TS), SIFRIM-HITZ-WEISS syndrome (SIHIWES) |
| #82 | TOF | – | – | dup | arr[hg19] 8p23.1(6,920,000–12,580,000) × 3 | 5.66 | P | – | 8p23.1 duplication syndrome |
| #84 | TOF | – | – | del | arr[hg19] 22q11.21(18,880,000–21,440,000) × 1 | 2.56 | P | PRODH | DIGEORGE syndrome; DGS (proximal, A-B)syndrome1, |
| #85 | VSD, IAA | – | – | del | arr[hg19] 22q11.21q11.23(18,564,800–24,300,000) × 1 | 3.2 | P | PEX26, TUBA8,PRODH | 22q11 deletion syndrome |
| #100 | TOF | – | – | del | arr[hg19] 22q11.21(18,970,561–21,800,471) × 1 | 2.8 | P | CLTCL1, HIRA,TBX1 | DiGeorgesyndrome(DGS), velocardio facial syndrome(VCFS) |
| #110 | Other CHD | – | Central nervous | del | arr[hg19] 7q33q36.3(137,754,586–159,119,707) × 1 | 21.4 | P | BRAF, CNTNAP2, DPP6 | Cardiofaciocutaneous syndrome-1, Noonan syndrome 7, |
| #110 | Other CHD | – | Central nervous | dup | arr[hg19] 20q13.2q13.33(51,222,942–62,913,645) × 3 | 11.7 | P | CYP24A1, PCK1,OSBPL2, RTEL1 |
HYPERCALCEMIA INFANTILE-1(HCINF1), phosphoenolpyruvate carboxykinase deficiency |
| #111 | VSD | – | – | del | arr[hg19] 16p11.2(29,428,531–30,190,029) × 1 | 0.74 | LP | PRRT2, KCTD13, TBX6, MAPK3 | 16p11.2deletion syndrome |
| #114 | AS | – | Skeletal system | del | arr[hg19] 22q11.21(18,631,364–21,800,471) × 1 | 3.2 | P | CLTCL1,HIRA,TBX1 |
DiGeorgesyndrome(DGS), velo- cardio- facial syndrome(VCFS) |
| #116 | CA, VSD, PLSVC | – | Cystic hygroma, Skeletal system | del | arr[hg19] 4p16.3p15.31(68,345–18,451,423) × 1 | 18.4 | P | LONP1, NFIX, SMARCA4 | BWS/SRS (Beckwith–Wiedemann syndrome/Silver-Russell syndrome;CODAS syndrome |
| #116 | CA, VSD, PLSVC | – | Cystic hygroma, Skeletal system | dup | arr[hg19] 11p15.5p15.1(230,680–20,167,667) × 3 | 19.9 | P | APC2,TICAM1, LONP1 |
Pigmented nodular adrenocortical diseaseprimarysyndrome; CODAS syndrome |
| #117 | Other CHD | Echogenic bowel | Skeletal system | del | arr[hg19] 15q11.2(22,770,421–23,277,436) × 1 | 0.50 | LP | TUBGCP5, CYFIP1, NIPA2, NIPA1 | 15q11.2 recurrent region (BP1-BP2) (includes NIPA1) deletionsyndrome1 |
| #120 | Other CHD | Choroid plexus cysts | Facial dysmorphisms | dup | arr[hg19] Xp22.31(6,455,151–8,135,568) × 3 | 1.68 | P | PUDP, STS, VCX, PNPLA4 | Steroid sulphatase deficiency (STS) |
| #121 | PAA,ASD | – | Urinary tract system, facial dysmorphisms | del | arr[hg19] 4q31.3(151,335,416–151,834,016) × 1 | 0.5 | LP | LRBA, MAB21L2 | – |
| #135 | CA | – | – | del | arr[hg19] 21q22.2q22.3(39,985,071–48,093,361) × 1 | 8.1 | P | KPTN | Autosomal recessive mental retardation-41 (MRT41) |
| #136 | VSD | – | – | dup | arr[hg19] 9q34.11q34.3(133,343,703–141,018,648) × 3 | 7.7 | P | – | – |
| #138 | AVSD | – | – | del | arr[hg19] 16q24.1q24.2(85,520,919–87,149,214) × 1 | 1.6 | P | FOXF1, FOXC2, FOXL1 | – |
| #157 | VSD, IAA | – | – | del | arr[hg19] 22q11.21(18,636,749–21,800,471) × 1 | 3.16 | P | CLTCL1, HIRA,TBX1 | DiGeorgesyndrome(DGS), velo- cardio- facial syndrome(VCFS) |
| #179 | VSD | – | – | del | arr[hg19] 15q11.2(22,770,421–23,625,785) × 1 | 0.83 | LP | TUBGCP5, CYFIP1, NIPA2, NIPA1 | 15q11.2 recurrent region (BP1-BP2)deletionsyndrome |
| #179 | VSD | – | – | del | arr[hg19] 16p13.11(14,910,158–16,520,463) × 1 | 1.6 | P | NOMO1, NPIPA1, PDXDC1, NTAN1), RRN3, KIAA0430, NDE1, MYH11, ABCC1, ABCC6, NOMO3 | 16p13.11 recurrent microdeletion syndrome |
CNVs found by CMA in the cohort, with the number of genes present in the region, listing the most relevant genes and phenotypes for each individual. Dup, Duplication; Del, Deletion; CA, congenital anomalies; LP, likely pathogenic; P, pathogenic; VOUS, variants of uncertain significance. VSD, ventricular septal defect; TGA, transposition of the great arteries; CA, coarctation of aorta; RAA, right aortic arch; ASD, atrial septum defect; AS, aortic stenosis; AVSD, atrioventricular septal defect; TOF, tetralogy of fallot; HLHS, hypoplastic left heart syndrome; IAA, interruption of aortic arch; PLSVC: persistent left superior vena cava; PAA: pulmonary artery atresia; PVS: pulmonary valve stenosis; DOLV: double outlet right ventricle