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Table 7 Pathogenic or likely pathogenic CNVs found in the cohort

From: Estimating the frequency of causal genetic variants in foetuses with congenital heart defects: a Chinese cohort study

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
  1. 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