Table 1.

Confirmed Rare De Novo CNVs in Discovery Cohort

IDChrStartEndBandCNV*Syndrome/GeneAnalysis ObservedCardiac Lesion: (Diagnosis)Parent OriginExtracardiacGenes, nSize, kb
1-01401159 247 99359 251 097p32.11JUNALVOT (HLHS)......13.1
1-031711145 586 403145 799 634q21.131q21.1 dup/GJA5A ECTD (TOF/APVS)......7213.2
1-010361146 631 133147 416 212q21.131q21.1 dup/GJA5ECTD (TOF)M...15785.1
1-014861194 201 171194 304 070q24.2–q253CDC73ALVOT (HLHS)...Yes0102.9
1-015181248 750 565248 795 110q443OR2T10, OR2T11ALVOT (HLHS)......244.5
1-01536270 168 99570 359 345p13.31PCBP1ACTD (TOF/PA)......5190.4
1-014012102 493 466103 001 458q11.2–q12.11MAP4K4ELVOT (HLHS)......6508.0
1-014012145 155 868145 274 931q22.31Mowat-Wilson/ZEB2ELVOT (HLHS)......1119.1
1-00762360 66111 712 230p26.13ARL8B, ARPC4, CAMK1, CAV3, CRBN, EMC3, ITPR1, SEC13, SETD5, VGLL4AASD/PS (ASD)...Yes10311651.6
1-01049315 637 81215 643 461p25.13BTD, HACL1ECTD (TOF)......25.6
1-010453477 80 96548 309 270p21.313CDC25A, DHX30, MAP4, SMARCC1ALVOT (HLHS)......14528.3
1-020933197 143 652197 186 111q293BDH1ACTD (TOF/PA)...Yes042.5
1-007714185 603 346185 638 397q34.11CENPU, PRIMPOLECTD (DTGA/VSD)PYes235.1
1-007895136 464232 969p15.333CCDC127, LRRC14B, PLEKHG4B, SDHAACTD (TOF)......496.5
1-001135133 706 994133 730 455q31.11UBE2BACTD (TOF/PA)...Yes123.5
1-002965166 386 727173 073 664q34–q35.21NKX2.5ACTD (TOF)MYes536686.9
1-01916636 646 78836 651 971p21.21CDKN1AAHTX (HTX)......15.2
1-01049643 484 78343 485 159p21.13POLR1CECTD (TOF)......10.4
1-00096750 179 70750 191 153p12.21C7orf72ECTD (TOF/PA)...Yes111.4
1-00800772 719 38674 138 603q11.231Williams syndromeACTD (VSD/PS)PYes341419.2
1-00540772 721 12374 140 708q11.231Williams syndromeALVOT (ASD)MYes341419.6
1-009777138 258 252143 807 632q24–q251C7orf55, FAM115A, LUC7L2, MKRN1, NDUFB2, UBN2, ZC3HAV1L, ZYXECTD (TOF)......1755549.4
1-019957142 334 207142 460 871q341MTRNR2L6, PRSS1ECTD (TOF)M...15126.7
1-0156288 067 76812 530 976p22.1–p23.13GATA4ACTD (TOF)......754463.2
1-0262588 102 18312 190 106p23.13GATA4ALVOT (CoA)MYes624087.9
1-00566811 606 42811 710 963p23.11GATA4A ECTD (TOF)......6104.5
1-009488119 053 343119 064 098q24.11EXT1ALVOT (CoA)PYes110.8
1-0236095 302 5005 337 760p24.13RLN1, RLN2ACTD (ASD)...Yes335.3
1-018521134 458 23034 460 862p131CATACTD (VSD)......12.6
1-005651142 968 28342 970 488p123HNRNPKP3ALVOTO (ASD)......02.2
1-015361165 157 23965 408 708q13.11EHBP1L1, LTBP3, MAP3K11, PCNXL3, SCYL1, SSSCA1ACTD (TOF/PA)......14251.5
1-002301186 939 59287 025 456q14.21TMEM135A ELVOT (ASD)PYes185.9
1-0148611125 641 368134 943 190q24.2–q251Jacobsen/ETS1A ELVOT (HLHS)PYes739301.8
1-0079511134 598 043134 617 838q253LOC283177ACTD (VSD)M...019.8
1-00124128 003 7588 123 306p13.313SLC2A14, SLC2A3ALVOT (ASD/HLHS)......3119.5
1-000501252 845 95252 862 783q13.131KRT6CALVOT (HLHS)......116.8
1-024111458 860 89358 881 694q23.11TIMM9, TOMM20LACTD (TOF)......220.8
1-010491474 551 63274 551 731q24.33LIN52ECTD (TOF)......10.1
1-001921522 296 98523 161 330q11.231 MB from PW/CYFIP1ALVOT (CoA)......20864.3
1-003151522 750 30523 140 114q11.231 MB from PW/CYFIP1ALVOT (CoA)M...5389.8
1-013961522 750 30523 228 712q11.211 MB from PW/CYFIP1A ECTD (TOF/PA)P...6478.4
1-002431522 835 89323 062 345q11.211 MB from PW/CYFIP1ELVOT (CoA)PYes4226.5
1-019941528 389 77128 446 734q13.21HERC2ELVOT (ASD)P...157.0
1-016961544 833 58844 856 873q21.11EIF3J, SPG11A ECTD (TriAtresia/DTGA)......223.3
1-019411588 761 53988 779 300q25.33NTRK3ACTD (TOF/DTGA)P-117.8
1-014271721 562 47322 252 439p11.21FAM27L, FLJ36000, MTRNR2L1AHTX (HTX)...Yes7690.0
1-005611727 962 39328 099 002q11.21SSH2ALVOT (ASD)...Yes3136.6
1-019951738 544 62438 548 586q21.11TOP2AA ECTD (TOF)......14.0
1-010491739 845 21039 846 477q21.23EIF1ECTD (TOF)......21.3
1-015881865 138 64278 015 180q22.1–q231NFATC1ALVOT (CoA)...Yes5812 876.5
1-021701920 601 00620 717 536p121ZNF826PACTD (TOF)...Yes1116.5
1-001741940 515 74440 681 387q13.21ZNF546, ZNF780A, ZNF780BACTD (TOF/PA)...Yes4165.6
1-015361947 792 29347 905 132q13.331C5AR1, C5AR2, DHX34ACTD (TOF/PA)......3112.8
1-007302014 529 65714 583 899p12.21MACROD2, MACROD2-IT1ACTD (DTGA)......254.2
1-011942218 844 63221 500 000q11.21DiGeorge/TBX1ACTD (VSD)PYes802655.4
1-001132218 886 91522 000 000q11.21DiGeorge/TBX1A ECTD (TOF/PA)PYes963113.1
1-018362219 020 52921 380 382q11.21DiGeorge/TBX1A ECTD (TOF)M...702359.9
1-009882220 733 49521 464 479q11.21DiGeorge/TBX1ACTD (HLHS/HTX)MYes31731.0
1-021332225 661 72525 919 492q11.23322q11 distal duplicationACTD (TOF)......4257.8
1-004252236 038 07636 149 338q12.31APOL5, APOL6, RBFOX2A ELVOT (HLHS)......4111.3
1-014272242 522 63842 531 210q13.23CYP2D6AHTX (HTX)...Yes28.6
1-01941X23 003 52523 086 619p22.113DDX53, RP11-40F8.2ACTD (TOF/DTGA)......183.1
1-00197X148 685 645148 693 146q283TMEM185AELVOT (HLHS)...Yes17.5
  • Genomic coordinates refer to hg19. APVS indicates absent pulmonary valve syndrome; ASD, atrial septal defect; CNV, copy number variant; CoA, coarctation of the aorta; CTD, conotruncal defect; DTGA, dextro-transposition of the great arteries; HLHS, hypoplastic left heart syndrome; HTX, heterotaxy; LVOT, left ventricular outflow tract obstruction; M, maternal chromosome; P, paternal chromosome; PA, pulmonary atresia; PS, pulmonary stenosis; TOF, tetralogy of Fallot; TriAtresia, tricuspid atresia; and VSD, ventricular septal defect.

  • * Copy number: 1, deletion and 3, duplication.

  • Analysis: A, identified with single nucleotide polymorphism array and E, identified with whole exome sequencing.

  • De novo CNV loci that were previously reported as pathogenic.