Conotruncal heart malformations

disease
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Also known as conotruncal cardiac defectsconotruncal heart malformations, variableCTHMTaussig-Bing syndrome or defect

Summary

Conotruncal heart malformations (MONDO:0016581) is a disease (an umbrella term covering 8 Mondo subtypes) caused by variants in NKX2-5 and TBX1, with 29 cohort genes (92 GWAS associations across 9 studies) and 3 clinical trials. The dominant Reactome pathway is Cardiogenesis (4 cohort genes). Top therapeutic interventions include calcium gluconate and sodium citrate.

At a glance

  • Causal genes: NKX2-5 (GenCC Definitive), TBX1 (GenCC Definitive)
  • Umbrella term: 8 Mondo subtypes
  • Cohort genes: 29
  • GWAS associations: 92
  • ClinVar variants: 180
  • Clinical trials: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical nameconotruncal heart malformations
Mondo IDMONDO:0016581
OMIM217095
Orphanet2445
SNOMED CT218728005
UMLSC1857586
MedGen341803
GARD0008189
Is cancer (heuristic)no

Also known as: conotruncal cardiac defects · conotruncal heart malformations · conotruncal heart malformations, variable · CTHM · Taussig-Bing syndrome or defect

Data availability: 180 ClinVar variants · 92 GWAS associations (9 studies) · 8 GenCC gene-disease records.

Disease family

An umbrella term covering 8 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › cardiovascular disordercongenital anomaly of cardiovascular systemcongenital heart malformationconotruncal heart malformations

Related subtypes (25): transposition of the great arteries, congenital left-sided heart lesions, interventricular septum aneurysm, congenital heart defects, multiple types, 2, coronary artery congenital malformation, criss-cross heart, triatrial heart, familial idiopathic dilatation of the right atrium, cardiac diverticulum, congenital mitral malformation, congenital pericardium anomaly, ectopia cordis, visceral heterotaxy, mesocardia, univentricular cardiopathy, congenital anomaly of the great arteries, Laubry-Pezzi syndrome, congenital Gerbode defect, juxtaposition of the atrial appendages, ectasia of the right atrial appendage, ectasia of the left appendage, atrial septal aneurysm, congenital acardia, congenital right-sided heart lesions, congenital heart defects, multiple types, 1, X-linked

Subtypes (8): pulmonary atresia with ventricular septal defect, tetralogy of fallot, abnormal origin of the pulmonary artery, congenital aortopulmonary window, persistent truncus arteriosus, double outlet right ventricle, double outlet left ventricle, pulmonary valve agenesis

Genetics & variants

GWAS landscape

92 GWAS associations across 9 studies. Top hits map to 30 distinct genes (as reported by GWAS).

Top associations by p-value

rsIDp-valueGeneRisk alleleOdds ratio
rs68862612e-07ANXA2R-OT1?1.78
rs558848722e-07TOX-DT - RNA5SP267?1.2
rs9215412e-07INSYN1-AS1 - TBC1D21?
rs110173283e-07Y_RNA - MIR378C?2.87
rs25175823e-07LINC02570?1.17
rs133533963e-07LINC01811?
rs744614734e-07SLC38A3?1.25
rs21089756e-07SHISA6?
rs134118406e-07ALK?
rs8391566e-07MGAT4C?
rs131021506e-07INPP4B?
rs65452788e-07GGCTP3 - CRTC1P1?2.62
rs171897638e-07SFTA2 - NAPGP2?1.04
rs789772948e-07LINC00536?
rs28133928e-07ADARB2?
rs19591229e-07RPL9P6 - EIF3LP1?7.63
rs22673861e-06KCNJ4?3.12
rs43664901e-06SLC22A24 - SLC22A25?1.7
rs67631591e-06CFAP20DC-DT?1.47
rs61400381e-06CASC20 - LINC01713?5.24
rs1461897031e-06ADAM29 - TSEN2P1?1.01
rs70243921e-06LINC03131 - JKAMPP1?2.01
rs77202061e-06ADGRV1?
rs64653871e-06CALCR?
rs110124621e-06NEBL?
rs68823801e-06ANXA2R-OT1?
rs69968021e-06RNU6-596P - RPL30P10?
rs38434301e-06LINC01182?
rs131771802e-06FEM1C - TICAM2?1.28
rs12177522e-06CARTPT - MAP1B?1.08

Top studies (by case count)

StudyLead authorYearCasesControlsTitle
GCST90026409Oluwafemi OO20219130Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States.
GCST90570534Broberg M2024404392,942Genome-wide association studies highlight novel risk loci for septal defects and left-sided congenital heart defects.
GCST013176Agopian AJ20194032,974X-chromosome association studies of congenital heart defects.
GCST90026410Oluwafemi OO20212942,976Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States.
GCST90026411Oluwafemi OO20212942,976Genome-Wide Association Studies of Conotruncal Heart Defects with Normally Related Great Vessels in the United States.
GCST013177Agopian AJ201900X-chromosome association studies of congenital heart defects.
GCST004720Agopian AJ201702,976Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects.
GCST004723Agopian AJ201700Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects.
GCST002438Agopian AJ201400Genome-wide association study of maternal and inherited loci for conotruncal heart defects.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

TierVariants
Tier 1: coding0
Tier 2: splice/UTR0
Tier 3: regulatory2
Tier 4: intronic/intergenic48

MAF distribution

BucketVariants
common (>=0.05)47
low_freq (0.01-0.05)2
rare (<0.01)0
unknown1

Functional consequences

ConsequenceCount
intron_variant35
intergenic_variant13
regulatory_region_variant2

Top variants

rsIDChrPosAllelesMAFConsequenceGenep-valueTier
rs6886261543022662T>C0.05intron_variantANXA2R-OT12e-07Tier 4: intronic/intergenic
rs55884872859280255C>A,G0.05intron_variantTOX-DT - RNA5SP2672e-07Tier 4: intronic/intergenic
rs9215411573867762C>A,G,T0.05intergenic_variantINSYN1-AS1 - TBC1D212e-07Tier 4: intronic/intergenic
rs1101732810130548836C>A,G,T0.05intergenic_variantY_RNA - MIR378C3e-07Tier 4: intronic/intergenic
rs2517582630840985C>A,G,T0.05intron_variantLINC025703e-07Tier 4: intronic/intergenic
rs13353396334505673T>A,C,G0.05intron_variantLINC018113e-07Tier 4: intronic/intergenic
rs74461473350213314C>T0.05intron_variantSLC38A34e-07Tier 4: intronic/intergenic
rs21089751711317850C>A0.05intron_variantSHISA66e-07Tier 4: intronic/intergenic
rs13411840229750415A>C,T0.05intron_variantALK6e-07Tier 4: intronic/intergenic
rs8391561286201912A>C,G,T0.05intron_variantMGAT4C6e-07Tier 4: intronic/intergenic
rs131021504142548980C>A0.05intron_variantINPP4B6e-07Tier 4: intronic/intergenic
rs6545278252478914T>G0.05intergenic_variantGGCTP3 - CRTC1P18e-07Tier 4: intronic/intergenic
rs17189763630955750C>T0.05regulatory_region_variantSFTA2 - NAPGP28e-07Tier 3: regulatory
rs789772948116396904C>T0.05intergenic_variantLINC005368e-07Tier 4: intronic/intergenic
rs2813392101586710A>C,G0.05intron_variantADARB28e-07Tier 4: intronic/intergenic
rs19591221481871321C>A,Tintron_variantRPL9P6 - EIF3LP19e-07Tier 4: intronic/intergenic
rs22673862238436107G>A0.024intron_variantKCNJ41e-06Tier 4: intronic/intergenic
rs43664901163145382T>A,C0.05intergenic_variantSLC22A24 - SLC22A251e-06Tier 4: intronic/intergenic
rs6763159359663795T>C0.05intron_variantCFAP20DC-DT1e-06Tier 4: intronic/intergenic
rs6140038206601515C>A,T0.011intergenic_variantCASC20 - LINC017131e-06Tier 4: intronic/intergenic
rs1461897034175023930T>A,C0.05intron_variantADAM29 - TSEN2P11e-06Tier 4: intronic/intergenic
rs7024392912165298C>A,G,T0.05intergenic_variantLINC03131 - JKAMPP11e-06Tier 4: intronic/intergenic
rs7720206590772392C>G,T0.05intron_variantADGRV11e-06Tier 4: intronic/intergenic
rs6465387793524748C>G,T0.05intron_variantCALCR1e-06Tier 4: intronic/intergenic
rs110124621020986424T>A,C0.05intron_variantNEBL1e-06Tier 4: intronic/intergenic
rs6882380542921599T>A0.05intron_variantANXA2R-OT11e-06Tier 4: intronic/intergenic
rs6996802857380819T>C0.05intergenic_variantRNU6-596P - RPL30P101e-06Tier 4: intronic/intergenic
rs3843430414099649T>A,C0.05intron_variantLINC011821e-06Tier 4: intronic/intergenic
rs131771805115544896G>A,C,T0.05regulatory_region_variantFEM1C - TICAM22e-06Tier 3: regulatory
rs1217752571956619A>T0.05intron_variantCARTPT - MAP1B2e-06Tier 4: intronic/intergenic

ClinVar germline variants

180 retrieved; paginated sample, class counts are floors:

101 uncertain significance, 37 likely benign, 26 conflicting classifications of pathogenicity, 6 likely pathogenic, 3 benign, 3 benign/likely benign, 1 likely pathogenic; risk factor, 1 pathogenic/likely pathogenic, 1 not provided, 1 pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
2690915NM_005257.6(GATA6):c.729_730del (p.Gly244fs)GATA6Pathogeniccriteria provided, single submitter
159257NM_004387.4(NKX2-5):c.783del (p.Ala262fs)NKX2-5Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3583188NM_005257.6(GATA6):c.1135+2T>CGATA6Likely pathogeniccriteria provided, multiple submitters, no conflicts
3899338NM_005257.6(GATA6):c.1135+1G>AGATA6Likely pathogeniccriteria provided, single submitter
1172828NM_001136271.3(NKX2-6):c.455dup (p.Gln153fs)NKX2-6Likely pathogenic; risk factorcriteria provided, multiple submitters, no conflicts
133345NM_001136271.3(NKX2-6):c.453_454insT (p.Lys152Ter)NKX2-6Likely pathogeniccriteria provided, single submitter
2432235NM_001136271.3(NKX2-6):c.568C>T (p.Gln190Ter)NKX2-6Likely pathogeniccriteria provided, single submitter
791NM_001136271.3(NKX2-6):c.451T>C (p.Phe151Leu)NKX2-6Likely pathogeniccriteria provided, single submitter
4075193NM_024665.7(TBL1XR1):c.1188_1205del (p.Ile397_Thr402del)TBL1XR1Likely pathogeniccriteria provided, single submitter
210542NM_153252.5(BRWD3):c.5101G>A (p.Gly1701Arg)BRWD3Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
30210NM_005257.6(GATA6):c.551G>A (p.Ser184Asn)GATA6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
412726NM_005257.6(GATA6):c.1663C>G (p.Pro555Ala)GATA6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
999815NM_005257.6(GATA6):c.660C>T (p.Gly220=)GATA6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
424319NM_000214.3(JAG1):c.3467T>C (p.Val1156Ala)JAG1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1019319NM_004387.4(NKX2-5):c.178G>C (p.Glu60Gln)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1021433NM_004387.4(NKX2-5):c.169G>T (p.Ala57Ser)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1377875NM_004387.4(NKX2-5):c.510G>C (p.Gln170His)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1439076NM_004387.4(NKX2-5):c.370A>G (p.Lys124Glu)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
156161NM_004387.4(NKX2-5):c.809G>A (p.Cys270Tyr)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
372743NM_004387.4(NKX2-5):c.356C>A (p.Ala119Glu)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
392351NM_004387.4(NKX2-5):c.827C>G (p.Ala276Gly)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
505440NM_004387.4(NKX2-5):c.111G>A (p.Leu37=)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
850796NM_004387.4(NKX2-5):c.188C>T (p.Ala63Val)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
939551NM_004387.4(NKX2-5):c.387C>A (p.Asn129Lys)NKX2-5Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1311053NM_001136271.3(NKX2-6):c.368G>A (p.Arg123His)NKX2-6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
534674NM_001136271.3(NKX2-6):c.276G>A (p.Gln92=)NKX2-6Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1114796NM_001379200.1(TBX1):c.941G>A (p.Arg314Gln)TBX1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
1934268NM_001379200.1(TBX1):c.1004C>T (p.Ala335Val)TBX1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2001091NM_001379200.1(TBX1):c.1342C>A (p.Pro448Thr)TBX1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
2086566NM_001379200.1(TBX1):c.170_229del (p.Pro57_Pro76del)TBX1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 51 · Orphanet: 51 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

GeneClassificationInheritanceDiseaseRecords
GATA6DefinitiveAutosomal dominantpancreatic hypoplasia-diabetes-congenital heart disease syndrome16
NKX2-5DefinitiveSemidominantconotruncal heart malformations17
TBX1DefinitiveAutosomal dominantconotruncal heart malformations6
GDF1StrongAutosomal dominantcongenital heart defects, multiple types, 68
NKX2-6StrongAutosomal recessivecongenital heart disease4

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
TBX1Orphanet:172722q11.2 duplication syndrome
TBX1Orphanet:3303Tetralogy of Fallot
TBX1Orphanet:56722q11.2 deletion syndrome
TBX1Orphanet:665044Common arterial trunk with aortic dominance
TBX1Orphanet:665058Common arterial trunk with pulmonary dominance and interrupted aortic arch
TBX1Orphanet:685017Combined immunodeficiency due to TBX1 deficiency
NKX2-5Orphanet:101351Familial isolated congenital asplenia
NKX2-5Orphanet:1479Atrial septal defect-atrioventricular conduction defects syndrome
NKX2-5Orphanet:1627Deletion 5q35 syndrome
NKX2-5Orphanet:2248Hypoplastic left heart syndrome
NKX2-5Orphanet:3303Tetralogy of Fallot
NKX2-5Orphanet:334Hereditary atrial fibrillation
NKX2-5Orphanet:402075Familial bicuspid aortic valve
NKX2-5Orphanet:871Hereditary progressive cardiac conduction defect
NKX2-5Orphanet:95712Thyroid ectopia
NKX2-5Orphanet:95713Athyreosis
NKX2-5Orphanet:99103Atrial septal defect, ostium secundum type
NKX2-6Orphanet:3303Tetralogy of Fallot
NKX2-6Orphanet:334Hereditary atrial fibrillation
NKX2-6Orphanet:3384Common arterial trunk
GATA6Orphanet:2140Congenital diaphragmatic hernia
GATA6Orphanet:2255Pancreatic hypoplasia-diabetes-congenital heart disease syndrome
GATA6Orphanet:3303Tetralogy of Fallot
GATA6Orphanet:334Hereditary atrial fibrillation
GATA6Orphanet:665044Common arterial trunk with aortic dominance
GATA6Orphanet:665058Common arterial trunk with pulmonary dominance and interrupted aortic arch
GATA6Orphanet:99067Complete atrioventricular septal defect with ventricular hypoplasia
GATA6Orphanet:99103Atrial septal defect, ostium secundum type
GDF1Orphanet:216718Isolated congenitally uncorrected transposition of the great arteries
GDF1Orphanet:3303Tetralogy of Fallot
GDF1Orphanet:97548Right isomerism
FOXP2Orphanet:209908Isolated childhood apraxia of speech
FOXP2Orphanet:2510617q31 microdeletion syndrome
BRWD3Orphanet:528084Non-specific syndromic intellectual disability
SLC38A3Orphanet:442835Non-specific early-onset epileptic encephalopathy
SMCHD1Orphanet:2250Hyposmia-nasal and ocular hypoplasia-hypogonadotropic hypogonadism syndrome
SMCHD1Orphanet:269Facioscapulohumeral dystrophy
TBL1XR1Orphanet:487825Pierpont syndrome
TBL1XR1Orphanet:520Acute promyelocytic leukemia
FHITOrphanet:422526Hereditary clear cell renal cell carcinoma
GATA4Orphanet:2510718p23.1 microdeletion syndrome
GATA4Orphanet:25151046,XY partial gonadal dysgenesis
GATA4Orphanet:3303Tetralogy of Fallot
GATA4Orphanet:334Hereditary atrial fibrillation
GATA4Orphanet:576232Partial atrioventricular septal defect with ventricular hypoplasia
GATA4Orphanet:99067Complete atrioventricular septal defect with ventricular hypoplasia
GATA4Orphanet:99068Complete atrioventricular septal defect-tetralogy of Fallot
GATA4Orphanet:99103Atrial septal defect, ostium secundum type
JAG1Orphanet:261600Alagille syndrome due to 20p12 microdeletion
JAG1Orphanet:261619Alagille syndrome due to a JAG1 point mutation

Cohort genes → proteins

29 cohort genes, 29 distinct canonical proteins.

Evidence partition

SubsetGenes
gwas_only19
multi_evidence10

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
TBX1HGNC:11592ENSG00000184058O43435T-box transcription factor TBX1gencc,clinvar
NKX2-5HGNC:2488ENSG00000183072P52952Homeobox protein Nkx-2.5gencc,clinvar
NKX2-6HGNC:32940ENSG00000180053A6NCS4Homeobox protein Nkx-2.6gencc,clinvar
GATA6HGNC:4174ENSG00000141448Q92908Transcription factor GATA-6gencc,clinvar
GDF1HGNC:4214ENSG00000130283P27539Embryonic growth/differentiation factor 1gencc
VARS1HGNC:12651ENSG00000204394P26640Valine–tRNA ligasegwas
FOXP2HGNC:13875ENSG00000128573O15409Forkhead box protein P2gwas
ENTPD4HGNC:14573ENSG00000197217Q9Y227Ectonucleoside triphosphate diphosphohydrolase 4clinvar
SCHIP1HGNC:15678ENSG00000151967P0DPB3Schwannomin-interacting protein 1gwas
ZNF343HGNC:16017ENSG00000088876Q6P1L6Zinc finger protein 343gwas
FEM1CHGNC:16933ENSG00000145780Q96JP0Protein fem-1 homolog Cgwas
BRWD3HGNC:17342ENSG00000165288Q6RI45Bromodomain and WD repeat-containing protein 3clinvar
SLC38A3HGNC:18044ENSG00000188338Q99624Sodium-coupled neutral amino acid transporter 3gwas
ATG2BHGNC:20187ENSG00000066739Q96BY7Autophagy-related protein 2 homolog Bgwas
GSKIPHGNC:20343ENSG00000100744Q9P0R6GSK3B-interacting proteingwas
CTSGHGNC:2532ENSG00000100448P08311Cathepsin Ggwas
SLC38A12HGNC:25984ENSG00000109066Q8NE00Putative sodium-coupled neutral amino acid transporter 12gwas
SLC22A24HGNC:28542ENSG00000197658Q8N4F4Steroid transmembrane transporter SLC22A24gwas
SMCHD1HGNC:29090ENSG00000101596A6NHR9Structural maintenance of chromosomes flexible hinge domain-containing protein 1gwas
KAZNHGNC:29173ENSG00000189337Q674X7Kazringwas
KLHL29HGNC:29404ENSG00000119771Q96CT2Kelch-like protein 29gwas
TBL1XR1HGNC:29529ENSG00000177565Q9BZK7F-box-like/WD repeat-containing protein TBL1XR1clinvar
IQCJHGNC:32406ENSG00000214216Q1A5X6IQ domain-containing protein Jgwas
FHITHGNC:3701ENSG00000189283P49789Bis(5’-adenosyl)-triphosphatasegwas
GATA4HGNC:4173ENSG00000136574P43694Transcription factor GATA-4clinvar
GTF2H4HGNC:4658ENSG00000213780Q92759General transcription factor IIH subunit 4gwas
JAG1HGNC:6188ENSG00000101384P78504Protein jagged-1clinvar
KCNJ4HGNC:6265ENSG00000168135P48050Inward rectifier potassium channel 4gwas
PAPPAHGNC:8602ENSG00000182752Q13219Pappalysin-1gwas

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
TBX1T-box transcription factor TBX1Transcription factor that plays a key role in cardiovascular development by promoting pharyngeal arch segmentation during embryonic development.
NKX2-5Homeobox protein Nkx-2.5Transcription factor required for the development of the heart and the spleen.
NKX2-6Homeobox protein Nkx-2.6Acts as a transcriptional activator.
GATA6Transcription factor GATA-6Transcriptional activator.
GDF1Embryonic growth/differentiation factor 1May mediate cell differentiation events during embryonic development.
VARS1Valine–tRNA ligaseCatalyzes the attachment of valine to tRNA(Val).
FOXP2Forkhead box protein P2Transcriptional repressor that may play a role in the specification and differentiation of lung epithelium.
ENTPD4Ectonucleoside triphosphate diphosphohydrolase 4Catalyzes the hydrolysis of nucleoside triphosphates and diphosphates in a calcium- or magnesium-dependent manner, with a preference for pyrimidines.
ZNF343Zinc finger protein 343May be involved in transcriptional regulation.
FEM1CProtein fem-1 homolog CSubstrate-recognition component of a Cul2-RING (CRL2) E3 ubiquitin-protein ligase complex of the DesCEND (destruction via C-end degrons) pathway, which recognizes a C-degron located at the extreme C terminus of target proteins, leading to…
BRWD3Bromodomain and WD repeat-containing protein 3Plays a role in the regulation of cell morphology and cytoskeletal organization.
SLC38A3Sodium-coupled neutral amino acid transporter 3Symporter that cotransports specific neutral amino acids and sodium ions, coupled to an H(+) antiporter activity.
ATG2BAutophagy-related protein 2 homolog BLipid transfer protein required for both autophagosome formation and regulation of lipid droplet morphology and dispersion.
GSKIPGSK3B-interacting proteinA-kinase anchoring protein for GSK3B and PKA that regulates or facilitates their kinase activity towards their targets.
CTSGCathepsin GSerine protease with trypsin- and chymotrypsin-like specificity.
SLC22A24Steroid transmembrane transporter SLC22A24Renal transmembrane organic anion/dicarboxylate exchanger that participates in the reabsorption of conjugated steroids including estradiol-17beta-D-glucuronide (or 17beta-estradiol 17-O-(beta-D-glucuronate)), androstanediol glucuronide (or…
SMCHD1Structural maintenance of chromosomes flexible hinge domain-containing protein 1Non-canonical member of the structural maintenance of chromosomes (SMC) protein family that plays a key role in epigenetic silencing by regulating chromatin architecture.
KAZNKazrinComponent of the cornified envelope of keratinocytes.
TBL1XR1F-box-like/WD repeat-containing protein TBL1XR1F-box-like protein involved in the recruitment of the ubiquitin/19S proteasome complex to nuclear receptor-regulated transcription units.
FHITBis(5’-adenosyl)-triphosphatasePossesses dinucleoside triphosphate hydrolase activity.
GATA4Transcription factor GATA-4Transcriptional activator that binds to the consensus sequence 5’-AGATAG-3’ and plays a key role in cardiac development and function.
GTF2H4General transcription factor IIH subunit 4Component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CAK, in RNA transcription…
JAG1Protein jagged-1Ligand for multiple Notch receptors and involved in the mediation of Notch signaling.
KCNJ4Inward rectifier potassium channel 4Inward rectifier potassium channels are characterized by a greater tendency to allow potassium to flow into the cell rather than out of it.
PAPPAPappalysin-1Metalloproteinase which specifically cleaves IGFBP-4 and IGFBP-5, resulting in release of bound IGF.

Protein-family classification

Druggable: 6 · Difficult: 10 · Unknown: 13 · Druggable fraction: 0.21

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

FamilyGenesFoldFDR
Transcription factor72.0×0.376
Ion channel13.9×0.410
Protease22.5×0.410
Scaffold/PPI31.8×0.410
Transporter12.7×0.438
Enzyme (other)20.8×0.827
Other/Unknown130.8×0.916

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
TBX1Transcription factornoTF_T-box, p53-like_TF_DNA-bd_sf, TF_T-box_CS
NKX2-5Transcription factornoHD, Homeodomain-like_sf, Homeobox_CS
NKX2-6Transcription factornoHD, Homeodomain-like_sf, Homeobox_CS
GATA6Transcription factornoZnf_GATA, GATA_N, Znf_NHR/GATA
GDF1Other/UnknownnoTGF-b_C, TGF-beta-like, TGFb_CS
VARS1Enzyme (other)yes6.1.1.9aa-tRNA-synth_I_CS, aa-tRNA-synth_Ia, Valyl-tRNA_ligase
FOXP2Transcription factornoFork_head_dom, TF_fork_head_CS_2, FOXP-CC
ENTPD4Other/UnknownnoGDA1_CD39_NTPase
SCHIP1Other/UnknownnoSCHIP_1_C, SCHIP_1
ZNF343Transcription factornoKRAB, Znf_C2H2_type, KRAB_dom_sf
FEM1CScaffold/PPInoAnkyrin_rpt, TPR-like_helical_dom_sf, Ankyrin_rpt-contain_sf
BRWD3Scaffold/PPInoBromodomain, WD40_rpt, WD40/YVTN_repeat-like_dom_sf
SLC38A3Other/UnknownnoAA_transpt_TM
ATG2BOther/UnknownnoATG2
GSKIPOther/UnknownnoGSKIP_dom, GSKIP_dom_sf, GSKIP
CTSGProteaseyes3.4.21.20Trypsin_dom, Peptidase_S1A, Peptidase_S1_PA
SLC38A12Other/UnknownnoAA_transpt_TM
SLC22A24TransporteryesMFS_sugar_transport-like, MFS_dom, MFS_trans_sf
SMCHD1Other/UnknownnoSMC_hinge, SMC_hinge_sf, HATPase_C_sf
KAZNOther/UnknownnoSAM, SAM/pointed_sf, Kazrin_SAM_rpt_1
KLHL29Other/UnknownnoBTB/POZ_dom, Kelch_1, SKP1/BTB/POZ_sf
TBL1XR1Scaffold/PPInoWD40_rpt, LisH, WD40/YVTN_repeat-like_dom_sf
IQCJOther/UnknownnoIQCJ-SCHIP1_N, IQ_domain_protein
FHITEnzyme (other)yes3.6.1.29HIT-like, Histidine_triad_CS, HIT-like_sf
GATA4Transcription factornoZnf_GATA, GATA_N, Znf_NHR/GATA
GTF2H4Other/UnknownnoTFIIH_p52/Tfb2, Tfb2_C
JAG1Other/UnknownnoEGF-type_Asp/Asn_hydroxyl_site, EGF, VWF_dom
KCNJ4Ion channelyesK_chnl_inward-rec_Kir2.3, K_chnl_inward-rec_Kir_cyto, Ig_E-set
PAPPAProteaseyes3.4.24.79Sushi_SCR_CCP_dom, Notch_dom, LamG-like

Expression context

Cohort genes with no expression data: 0.

24 cohort genes are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)2
broad (>20)27
unknown0

Top tissues across cohort

TissueCohort genes
middle temporal gyrus4
calcaneal tendon4
right atrium auricular region3
buccal mucosa cell3
tibia3
hindlimb stylopod muscle2
jejunal mucosa2
sural nerve2
tibialis anterior2
Brodmann (1909) area 232
secondary oocyte2
sperm2
right lobe of liver2
upper leg skin2
gastrocnemius1
muscle of leg1
apex of heart1
cardiac atrium1
minor salivary gland1
saliva-secreting gland1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
TBX1220broadmarkerhindlimb stylopod muscle, gastrocnemius, muscle of leg
NKX2-598broadyesapex of heart, right atrium auricular region, cardiac atrium
NKX2-613tissue_specificyesright atrium auricular region, minor salivary gland, saliva-secreting gland
GATA6204ubiquitousmarkergerminal epithelium of ovary, parietal pleura, jejunal mucosa
GDF134ubiquitousyesprimary visual cortex, sural nerve, superior frontal gyrus
VARS1134ubiquitousmarkerright testis, left testis, testis
FOXP2237broadmarkerbuccal mucosa cell, tibialis anterior, mucosa of paranasal sinus
ENTPD4291ubiquitousmarkerBrodmann (1909) area 23, middle temporal gyrus, tibia
SCHIP1133ubiquitousmarkerventricular zone, prefrontal cortex, Brodmann (1909) area 9
ZNF343206ubiquitousmarkertibialis anterior, secondary oocyte, calcaneal tendon
FEM1C259ubiquitousmarkersperm, male germ cell, skeletal muscle tissue of biceps brachii
BRWD3223ubiquitousmarkertendon of biceps brachii, epithelial cell of pancreas, calcaneal tendon
SLC38A3164broadmarkerright lobe of liver, hindlimb stylopod muscle, liver
ATG2B282ubiquitousmarkerBrodmann (1909) area 23, middle temporal gyrus, sperm
GSKIP255ubiquitousmarkersecondary oocyte, ileal mucosa, jejunal mucosa
CTSG194broadmarkertrabecular bone tissue, bone marrow cell, bone marrow
SLC38A12211ubiquitousmarkerstromal cell of endometrium, granulocyte, monocyte
SLC22A2411markerbuccal mucosa cell, adult mammalian kidney, upper leg skin
SMCHD1290ubiquitousmarkercalcaneal tendon, colonic epithelium, blood
KAZN277ubiquitousmarkercerebellar vermis, inferior vagus X ganglion, esophagus squamous epithelium
KLHL29256ubiquitousmarkertibia, middle temporal gyrus, sural nerve
TBL1XR1284ubiquitousmarkercalcaneal tendon, nipple, tibia
IQCJ46tissue_specificmarkermale germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad, corpus callosum
FHIT188ubiquitousmarkerright adrenal gland, right adrenal gland cortex, left adrenal gland cortex
GATA485broadmarkerright atrium auricular region, heart left ventricle, duodenum
GTF2H4139ubiquitousyesright lobe of liver, pituitary gland, metanephros cortex
JAG1297ubiquitousmarkerupper leg skin, skin of hip, blood vessel layer
KCNJ4119yesendothelial cell, middle temporal gyrus, Brodmann (1909) area 10
PAPPA244broadmarkerdecidua, placenta, buccal mucosa cell

Protein interactions among cohort

Intra-cohort edges: 7.

Hub genes (top 10 by interactor count)

SymbolInteractor count
VARS15,848
GATA44,994
JAG14,405
TBL1XR14,066
BRWD32,714
FOXP22,557
CTSG2,478
NKX2-52,355
KCNJ41,894
SMCHD11,888

Intra-cohort edges

ABSources
ATG2BGSKIPstring_interaction
GATA4NKX2-5biogrid_interaction, intact, string_interaction
GATA4NKX2-6string_interaction
GDF1NKX2-6string_interaction
NKX2-5TBX1string_interaction
NKX2-6TBX1string_interaction
SLC22A24ZNF343string_interaction

Structural data

PDB: 15 · AlphaFold-only: 14 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
GTF2H4Q9275951
CTSGP0831116
FEM1CQ96JP012
FHITP497899
PAPPAQ132198
JAG1P785047
NKX2-5P529524
GATA4P436943
FOXP2O154092
TBX1O434351
ENTPD4Q9Y2271
GSKIPQ9P0R61
SMCHD1A6NHR91
TBL1XR1Q9BZK71
KCNJ4P480501

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
VARS1P2664088.12
SLC22A24Q8N4F487.62
SLC38A12Q8NE0081.33
SLC38A3Q9962478.62
GDF1P2753974.44
KLHL29Q96CT271.27
KAZNQ674X771.09
ZNF343Q6P1L667.58
ATG2BQ96BY765.72
BRWD3Q6RI4565.11
NKX2-6A6NCS464.31
SCHIP1P0DPB361.13
GATA6Q9290853.48
IQCJQ1A5X649.01

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 186. Enrichment computed across 29 evidence-associated genes (18 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 18 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Cardiogenesis494.0×1e-05TBX1, NKX2-5, GATA6, GATA4
YAP1- and WWTR1 (TAZ)-stimulated gene expression284.6×0.015NKX2-5, GATA4
Formation of definitive endoderm279.3×0.015GATA6, GATA4
Physiological factors274.6×0.015NKX2-5, GATA4
Developmental Lineage of Multipotent Pancreatic Progenitor Cells266.8×0.015GATA6, GATA4
Signaling by NOTCH1 PEST Domain Mutants in Cancer245.3×0.020TBL1XR1, JAG1
Signaling by NOTCH1 in Cancer245.3×0.020TBL1XR1, JAG1
Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer245.3×0.020TBL1XR1, JAG1
Signaling by NOTCH1239.6×0.023TBL1XR1, JAG1
Constitutive Signaling by NOTCH1 PEST Domain Mutants221.9×0.062TBL1XR1, JAG1
Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants221.9×0.062TBL1XR1, JAG1
Signaling by NOTCH219.5×0.071TBL1XR1, JAG1
Classical Kir channels1158.6×0.084KCNJ4
Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant1158.6×0.084JAG1
Formation of lateral plate mesoderm1126.9×0.097GATA4
Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant190.6×0.097JAG1
Loss of MECP2 binding ability to the NCoR/SMRT complex190.6×0.097TBL1XR1
Suppression of apoptosis190.6×0.097CTSG
Phosphate bond hydrolysis by NTPDase proteins179.3×0.097ENTPD4
Loss of function of MECP2 in Rett syndrome179.3×0.097TBL1XR1
Pervasive developmental disorders179.3×0.097TBL1XR1
Response of Mtb to phagocytosis179.3×0.097CTSG
Disorders of Developmental Biology179.3×0.097TBL1XR1
Disorders of Nervous System Development179.3×0.097TBL1XR1
Signaling by NOTCH1 HD Domain Mutants in Cancer170.5×0.097JAG1
Interleukin-1 processing170.5×0.097CTSG
G protein gated Potassium channels163.4×0.097KCNJ4
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation163.4×0.097GATA6
Infection with Mycobacterium tuberculosis163.4×0.097CTSG
Cell recruitment (pro-inflammatory response)163.4×0.097CTSG

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 27 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
atrioventricular node development3312.1×2e-05NKX2-5, GATA6, GATA4
atrial cardiac muscle cell development2416.1×8e-04NKX2-5, NKX2-6
pharyngeal system development389.2×8e-04TBX1, NKX2-5, NKX2-6
outflow tract septum morphogenesis372.0×8e-04TBX1, NKX2-5, GATA6
epithelial cell differentiation426.0×0.001TBX1, NKX2-5, NKX2-6, GATA6
aortic valve morphogenesis348.0×0.002NKX2-5, GATA4, JAG1
atrioventricular canal development2113.5×0.005GATA6, GATA4
ventricular cardiac muscle cell development2113.5×0.005NKX2-5, NKX2-6
intestinal epithelial cell differentiation2113.5×0.005GATA6, GATA4
cardiac right ventricle morphogenesis2104.0×0.005GATA4, JAG1
atrial septum morphogenesis296.0×0.005NKX2-5, GATA4
cardiac septum morphogenesis289.2×0.005NKX2-5, JAG1
negative regulation of epithelial cell apoptotic process289.2×0.005NKX2-5, NKX2-6
positive regulation of epithelial cell proliferation327.1×0.005TBX1, NKX2-5, NKX2-6
positive regulation of transcription by RNA polymerase II84.4×0.006TBX1, NKX2-5, NKX2-6, GATA6, SLC38A3, TBL1XR1, GATA4, JAG1
aorta morphogenesis265.7×0.008TBX1, JAG1
epithelial cell apoptotic process262.4×0.009NKX2-5, NKX2-6
embryonic heart tube development256.7×0.010NKX2-5, NKX2-6
Purkinje myocyte differentiation1624.1×0.013NKX2-5
septum secundum development1624.1×0.013NKX2-5
diadenosine triphosphate catabolic process1624.1×0.013FHIT
caudate nucleus development1624.1×0.013FOXP2
putamen development1624.1×0.013FOXP2
negative regulation of transforming growth factor beta2 production1624.1×0.013GATA6
tube morphogenesis1624.1×0.013GATA6
sterol transmembrane transport1624.1×0.013SLC22A24
endocardial cushion cell development1624.1×0.013JAG1
regulation of transmembrane receptor protein serine/threonine kinase signaling pathway1624.1×0.013GDF1
biofilm matrix disassembly1624.1×0.013CTSG
L-asparagine import across plasma membrane1624.1×0.013SLC38A3

Therapeutics

Drug target analysis

Approved (phase 4): 1 · Phase ≥3: 2 · Phased (≥1): 3 · Undrugged: 26

Druggability breadth: 11 of 29 evidence-associated genes (38%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
CTSGBORTEZOMIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
CTSG54
SMCHD112
FHIT13
TBX100
NKX2-500
NKX2-600
GATA600
GDF100
VARS100
FOXP200

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
BORTEZOMIB4CTSG
TRIAMTERENE4CTSG
SURAMIN3FHIT
DELANZOMIB2CTSG
FULACIMSTAT2CTSG
ALOXISTATIN2CTSG
MOLIBRESIB2SMCHD1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 4.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
CTSG160Binding:155, ADMET:4, Toxicity:1
FHIT21Binding:19, ADMET:2
VARS17Binding:7
SMCHD17Binding:7
KCNJ47Binding:7
BRWD35Binding:5
GATA45Binding:5
TBL1XR12Binding:2
ENTPD41ADMET:1
GSKIP1Binding:1
JAG11Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
VARS16.1.1.9valine-tRNA ligase
CTSG3.4.21.20cathepsin G
FHIT3.6.1.29bis(5’-adenosyl)-triphosphatase
PAPPA3.4.24.79pappalysin-1

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
CTSG160

Pharmacogenomics

Cohort genes with a PharmGKB record: 29; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

7 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

CompoundMax phaseCohort target (bioactivity)
BORTEZOMIB4CTSG
TRIAMTERENE4CTSG
SURAMIN3FHIT
DELANZOMIB2CTSG
FULACIMSTAT2CTSG
ALOXISTATIN2CTSG
MOLIBRESIB2SMCHD1

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

TierDefinitionGenesSymbols
AApproved (phase 4 drug)1CTSG
BPhased (≥1) drug, not yet approved2SMCHD1, FHIT
CDruggable family + PDB, no drug2KCNJ4, PAPPA
DDruggable family + AlphaFold only, no drug2VARS1, SLC22A24
EDifficult family or no structure, no drug22TBX1, NKX2-5, NKX2-6, GATA6, GDF1, FOXP2, ENTPD4, SCHIP1, ZNF343, FEM1C (+12 more)

Undrugged target profiles

26 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

SymbolChEMBL assaysDrugged partners (top 3)
TBX10
NKX2-50
NKX2-60
GATA60
GDF10
VARS17
FOXP20
ENTPD41
SCHIP10
ZNF3430
FEM1C0
BRWD35
SLC38A30
ATG2B0
GSKIP1
SLC38A120
SLC22A240
KAZN0
KLHL290
TBL1XR12
IQCJ0
GATA45
GTF2H40
JAG11
KCNJ47
PAPPA0

Clinical trials & evidence

Clinical trials

Clinical trials: 3.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified3

Top trials by phase / activity

NCTPhaseStatusTitle
NCT00004361Not specifiedCOMPLETEDStudy of the Relationship Between Calcium Levels and Intact Parathyroid Hormone (iPTH) in Adults With Repaired or Palliated Conotruncal Cardiac Defects
NCT00005102Not specifiedUNKNOWNImmunologic Evaluation in Patients With DiGeorge Syndrome or Velocardiofacial Syndrome
NCT01460316Not specifiedCOMPLETEDConotruncal Cardiac Defects and Nutrigenetic Etiopathogeny

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
CALCIUM GLUCONATE41
SODIUM CITRATE41