# Tetralogy of Fallot: Genetic, Epigenetic and Clinical Insights into a Multifactorial Congenital Heart Disease

**Authors:** Maria Felicia Gagliardi, Emanuele Micaglio, Angelo Micheletti, Sara Benedetti, Diana Gabriela Negura, Francesca Bevilacqua, Giulia Guglielmi, Giulia Pasqualin, Alessandro Giamberti, Massimo Chessa

PMC · DOI: 10.3390/genes17020181 · Genes · 2026-01-31

## TL;DR

This review explores the genetic and epigenetic factors behind Tetralogy of Fallot, a heart defect, and how they influence its varied symptoms and treatment.

## Contribution

The paper integrates recent genomic and clinical findings to highlight the interplay of genetic and epigenetic mechanisms in Fallot-type heart defects.

## Key findings

- Variants in genes like NOTCH1, FLT4, and GATA6 are linked to conotruncal development and heart defects.
- Epigenetic factors such as DNA methylation and non-coding RNA influence the variability of Fallot-type malformations.
- New candidate genes and regulatory networks are emerging as key contributors to cardiac morphogenesis.

## Abstract

Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease, classically characterized by right ventricular outflow tract obstruction, ventricular septal defect, overriding aorta, and right ventricular hypertrophy. Recent advances in molecular and genomic research indicate that TOF is part of a phenotypic continuum encompassing Trilogy, Tetralogy, and Pentalogy of Fallot, in which the variability of anatomical presentation reflects shared genetic and epigenetic mechanisms with highly variable penetrance and expressivity. Variants in NOTCH1, FLT4, KDR, GATA6, and TBX1 highlight key pathways in conotruncal development and endothelial–mesenchymal transition, yet these well-known genes explain only a fraction of the genetic landscape. Emerging studies have identified additional candidate genes and networks involved in cardiac morphogenesis, including transcriptional regulators, signaling mediators, chromatin-remodeling factors, and splicing-associated genes such as PUF60 and DVL3. Epigenetic mechanisms, including DNA methylation, histone modifications, and non-coding RNA expression, further modulate phenotypic expressivity and contribute to variability along the Trilogy–Tetralogy–Pentalogy spectrum. This review integrates current genomic and clinical evidence to provide a comprehensive overview of the molecular architecture of Fallot-type conotruncal malformations, emphasizing the interplay between genetic and epigenetic mechanisms, genotype–phenotype correlations, and implications for diagnosis, risk stratification, counseling, and personalized management in the era of precision cardiology.

## Linked entities

- **Genes:** NOTCH1 (notch receptor 1) [NCBI Gene 4851], FLT4 (fms related receptor tyrosine kinase 4) [NCBI Gene 2324], KDR (kinase insert domain receptor) [NCBI Gene 3791], GATA6 (GATA binding protein 6) [NCBI Gene 2627], TBX1 (T-box transcription factor 1) [NCBI Gene 6899], PUF60 (poly(U) binding splicing factor 60) [NCBI Gene 22827], DVL3 (dishevelled segment polarity protein 3) [NCBI Gene 1857]
- **Diseases:** Tetralogy of Fallot (MONDO:0008542)

## Full-text entities

- **Genes:** PUF60 (poly(U) binding splicing factor 60) [NCBI Gene 22827] {aka FIR, RoBPI, SIAHBP1, VRJS}, JAG1 (jagged canonical Notch ligand 1) [NCBI Gene 182] {aka AGS, AGS1, AHD, AWS, CD339, CMT2HH}, DGCR8 (DGCR8 microprocessor complex subunit) [NCBI Gene 54487] {aka C22orf12, DGCRK6, Gy1, pasha}, CHD7 (chromodomain helicase DNA binding protein 7) [NCBI Gene 55636] {aka CRG, HH5, IS3, KAL5}, MALAT1 (metastasis associated lung adenocarcinoma transcript 1) [NCBI Gene 378938] {aka HCN, LINC00047, NCRNA00047, NEAT2, PRO2853, miPEP-52}, FLNA (filamin A) [NCBI Gene 2316] {aka ABP-280, ABPX, CSBS, CVD1, FGS2, FLN}, FKBP10 (FKBP prolyl isomerase 10) [NCBI Gene 60681] {aka BRKS, BRKS1, FKBP65, OI11, OI6, PPIASE}, HAND1 (heart and neural crest derivatives expressed 1) [NCBI Gene 9421] {aka Hxt, Thing1, bHLHa27, eHand}, IGF2 (insulin like growth factor 2) [NCBI Gene 3481] {aka C11orf43, GRDF, IGF-II, PP9974, SRS3}, SFRP1 (secreted frizzled related protein 1) [NCBI Gene 6422] {aka FRP, FRP-1, FRP1, FrzA, SARP2}, GATA6 (GATA binding protein 6) [NCBI Gene 2627], PTK7 (protein tyrosine kinase 7 (inactive)) [NCBI Gene 5754] {aka CCK-4, CCK4}, VEGFA (vascular endothelial growth factor A) [NCBI Gene 7422] {aka L-VEGF, MVCD1, VEGF, VPF}, PRCP (prolylcarboxypeptidase) [NCBI Gene 5547] {aka HUMPCP, PCP}, NOTCH1 (notch receptor 1) [NCBI Gene 4851] {aka AOS5, AOVD1, TAN1, hN1}, KMT2D (lysine methyltransferase 2D) [NCBI Gene 8085] {aka AAD10, ALR, BCAHH, CAGL114, KABUK1, KMS}, GNE (glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase) [NCBI Gene 10020] {aka DMRV, GLCNE, IBM2, NM, THC12, Uae1}, CDC45 (cell division cycle 45) [NCBI Gene 8318] {aka CDC45L, CDC45L2, MGORS7, PORC-PI-1}, QRSL1 (glutaminyl-tRNA amidotransferase subunit QRSL1) [NCBI Gene 55278] {aka COXPD40, GatA}, ISL1 (ISL LIM homeobox 1) [NCBI Gene 3670] {aka ISLET1, Isl-1}, HAND2 (heart and neural crest derivatives expressed 2) [NCBI Gene 9464] {aka DHAND2, Hed, Thing2, bHLHa26, dHand}, MEIS2 (Meis homeobox 2) [NCBI Gene 4212] {aka CPCMR, HsT18361, MRG1}, FLRT2 (fibronectin leucine rich transmembrane protein 2) [NCBI Gene 23768], H19 (H19 imprinted maternally expressed transcript) [NCBI Gene 283120] {aka ASM, ASM1, BWS, D11S813E, GMRSP, LINC00008}, KDR (kinase insert domain receptor) [NCBI Gene 3791] {aka CD309, FLK1, VEGFR, VEGFR2}, AKT1 (AKT serine/threonine kinase 1) [NCBI Gene 207] {aka AKT, PKB, PKB-ALPHA, PRKBA, RAC, RAC-ALPHA}, MYH6 (myosin heavy chain 6) [NCBI Gene 4624] {aka ASD3, CMD1EE, CMH14, MYHC, MYHCA, SSS3}, DVL3 (dishevelled segment polarity protein 3) [NCBI Gene 1857] {aka DRS3}, DYNC2H1 (dynein cytoplasmic 2 heavy chain 1) [NCBI Gene 79659] {aka ATD3, DHC1b, DHC2, DNCH2, DYH1B, SRPS2B}, TBX5 (T-box transcription factor 5) [NCBI Gene 6910] {aka HOS}, HIRA (histone cell cycle regulator) [NCBI Gene 7290] {aka DGCR1, TUP1, TUPLE1}, SHF (Src homology 2 domain containing F) [NCBI Gene 90525], MEF2C (myocyte enhancer factor 2C) [NCBI Gene 4208] {aka C5DELq14.3, DEL5q14.3, NEDHSIL}, DNAH11 (dynein axonemal heavy chain 11) [NCBI Gene 8701] {aka CILD7, DNAHBL, DNAHC11, DNHBL, DPL11}, FSD1L (fibronectin type III and SPRY domain containing 1 like) [NCBI Gene 83856] {aka CCDC10, CSDUFD1, FSD1CL, FSD1NL, MIR1}, SUCNR1 (succinate receptor 1) [NCBI Gene 56670] {aka GPR91}, FLT4 (fms related receptor tyrosine kinase 4) [NCBI Gene 2324] {aka CHTD7, FLT-4, FLT41, LMPH1A, LMPHM1, PCL}, FGF8 (fibroblast growth factor 8) [NCBI Gene 2253] {aka AIGF, FGF-8, HBGF-8, HH6, KAL6}, SOS1 (SOS Ras/Rac guanine nucleotide exchange factor 1) [NCBI Gene 6654] {aka GF1, GGF1, GINGF, HGF, NS4, SOS-1}, PIK3CB (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta) [NCBI Gene 5291] {aka P110BETA, PI3K, PI3KBETA, PIK3C1}, GATA4 (GATA binding protein 4) [NCBI Gene 2626] {aka ASD2, TACHD, TOF, VSD1}, PDGFRA (platelet derived growth factor receptor alpha) [NCBI Gene 5156] {aka CD140A, PDGFR-2, PDGFR2}, SOX11 (SRY-box transcription factor 11) [NCBI Gene 6664] {aka CSS9, IDDMOH, MRD27}, MIR424 (microRNA 424) [NCBI Gene 494336] {aka MIR322, MIRN424, hsa-mir-424, miRNA424, mir-424}, PTPN11 (protein tyrosine phosphatase non-receptor type 11) [NCBI Gene 5781] {aka BPTP3, CFC, JMML, METCDS, NS1, PTP-1D}, NFATC1 (nuclear factor of activated T cells 1) [NCBI Gene 4772] {aka NF-ATC, NF-ATc1.2, NFAT2, NFATc}, SHH (sonic hedgehog signaling molecule) [NCBI Gene 6469] {aka HHG1, HLP3, HPE3, MCOPCB5, SMMCI, ShhNC}, GJA1 (gap junction protein alpha 1) [NCBI Gene 2697] {aka AVSD3, CMDR, CX43, EKVP, EKVP3, GJAL}, TBX1 (T-box transcription factor 1) [NCBI Gene 6899] {aka CAFS, CATCH22, CTHM, DGCR, DGS, DORV}, PRICKLE1 (prickle planar cell polarity protein 1) [NCBI Gene 144165] {aka EPM1B, RILP}, MST1R (macrophage stimulating 1 receptor) [NCBI Gene 4486] {aka CD136, CDw136, NPCA3, PTK8, RON, SEA}, MAPK1 (mitogen-activated protein kinase 1) [NCBI Gene 5594] {aka ERK, ERK-2, ERK2, ERT1, MAPK2, NS13}, HOTAIR (HOX transcript antisense RNA) [NCBI Gene 100124700] {aka HOXAS, HOXC-AS4, HOXC11-AS1, NCRNA00072}, NKX2-5 (NK2 homeobox 5) [NCBI Gene 1482] {aka CHNG5, CSX, CSX1, HLHS2, NKX2.5, NKX2E}, NOTCH2 (notch receptor 2) [NCBI Gene 4853] {aka AGS2, HJCYS, hN2}, C2CD3 (C2 domain containing 3 centriole elongation regulator) [NCBI Gene 26005] {aka OFD14}, KRAS (KRAS proto-oncogene, GTPase) [NCBI Gene 3845] {aka 'C-K-RAS, C-K-RAS, CFC2, K-RAS2A, K-RAS2B, K-RAS4A}, OFD1 (OFD1 centriole and centriolar satellite protein) [NCBI Gene 8481] {aka 71-7A, CXorf5, JBTS10, RP23, SGBS2}, NOTCH4 (notch receptor 4) [NCBI Gene 4855] {aka INT3}, CRKL (CRK like proto-oncogene, adaptor protein) [NCBI Gene 1399]
- **Diseases:** myocardial vulnerability (MESH:D009202), diaphragmatic defects (MESH:D065630), biliary malformations (MESH:C537726), facial dysmorphisms (MESH:C565579), aortic arch anomalies (MESH:C535542), hypoxic (MESH:D002534), structural malformations (MESH:D020914), conotruncal malalignment (MESH:D017760), Robinow syndrome (MESH:C562492), epigenetic disorders (MESH:D009358), pulmonary stenosis (MESH:D011666), hypoxemia (MESH:D000860), RVOT obstruction (MESH:D000092243), Fallot (MESH:D013771), imprinting diseases (MESH:C567357), genetic defect (MESH:D030342), congenital cardiac malformations (MESH:C535853), pulmonary valve hypoplasia (MESH:D011665), CHARGE syndrome (MESH:D058747), ventricular septal defect (MESH:D006345), Fallot-type conotruncal malformations (MESH:C535464), Mitochondrial Dysfunction (MESH:D028361), short stature (MESH:D006130), congenital malformation (OMIM:163000), atrioventricular septal defects (MESH:C562831), atrial septal defect (MESH:D006344), injury to (MESH:D014947), anxiety (MESH:D001007), neurological complications (MESH:D002493), ocular anomalies (MESH:D005124), Pentalogy of Fallot (MESH:D058502), cyanosis (MESH:D003490), Chromosomal abnormalities (MESH:D002869), Alagille (MESH:D016738), Down syndrome (MESH:D004314), overriding aorta (MESH:D000784), dysmorphism (MESH:D057215), hepatic and vascular involvement (MESH:D056486), aortic root dilation (MESH:D000094628), right ventricular hypertrophy (MESH:D017380), septation defects (MESH:D000093665), cardiac defects (MESH:D006331), thymic hypoplasia (MESH:D013953), Sporadic (MESH:D020821), macrocephaly (MESH:D058627), Noonan spectrum disorders (MESH:D009634), ciliary dysfunction (MESH:D002925), septal defect (MESH:D006343), genital anomalies (MESH:D014564), Trilogy (MESH:D014286), chromosomal syndrome (MESH:D025063), velopharyngeal insufficiency (MESH:D014681), syndromic condition (MESH:D002908), pancreatic agenesis (MESH:C564908), abnormal cardiac morphogenesis (MESH:D018376), malformations (MESH:C564254), Verheij syndrome (OMIM:615583), conotruncal abnormal development (MESH:D002658), cerebral injury (MESH:D000070625), brain injury (MESH:D001930)
- **Chemicals:** ATP (MESH:D000255), calcium (MESH:D002118), retinoic acid (MESH:D014212)
- **Species:** Mus musculus (house mouse, species) [taxon 10090], Homo sapiens (human, species) [taxon 9606]

## Full text

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## Figures

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## References

44 references — full list in the complete paper: https://tomesphere.com/paper/PMC12940485/full.md

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Source: https://tomesphere.com/paper/PMC12940485