Malignant colon neoplasm

disease
On this page

Also known as cancer of coloncolon cancercolon neoplasm, malignantcolon tumor, malignantmalignant colon tumormalignant colon tumourmalignant colonic neoplasmmalignant colonic tumormalignant colonic tumourmalignant neoplasm of colonmalignant neoplasm of the colonmalignant tumor of colonmalignant tumor of the colonmalignant tumour of colonmalignant tumour of the colon

Summary

Malignant colon neoplasm (MONDO:0021063) is a cancer (an umbrella term covering 9 Mondo subtypes) with 18 cohort genes (15 CIViC-evidence somatic drivers; 32 ClinVar predisposition records) and 1,079 clinical trials. The dominant Reactome pathway is Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) (4 cohort genes). Molecularly, KRAS G13D confers sensitivity to Cetuximab in Colon Cancer (CIViC Level B); 20 further subtype–drug associations are mapped below. Top therapeutic interventions include leucovorin, panitumumab, and tipiracil.

At a glance

  • Classification: Cancer
  • Umbrella term: 9 Mondo subtypes
  • Cohort genes: 18
  • ClinVar variants: 32
  • Clinical trials: 1,079
  • Precision-medicine evidence (CIViC): 21 subtype–drug associations

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namemalignant colon neoplasm
Mondo IDMONDO:0021063
DOIDDOID:219
ICD-10-CMC18
ICD-111265576634
NCITC9242
SNOMED CT363406005
UMLSC0007102
MedGen2839
Anatomy (UBERON)UBERON:0001155
Is cancer (heuristic)yes

Also known as: cancer of colon · colon cancer · colon neoplasm, malignant · colon tumor, malignant · malignant colon neoplasm · malignant colon tumor · malignant colon tumour · malignant colonic neoplasm · malignant colonic tumor · malignant colonic tumour · malignant neoplasm of colon · malignant neoplasm of the colon · malignant tumor of colon · malignant tumor of the colon · malignant tumour of colon · malignant tumour of the colon

Data availability: 32 ClinVar variants.

Disease family

An umbrella term covering 9 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › digestive system disorderintestinal disorder › large intestine disorder › colonic disordercolonic neoplasmmalignant colon neoplasm

Related subtypes (7): benign colon neoplasm, colon neuroendocrine neoplasm, cecal neoplasm, colon inflammatory polyp, colon juvenile polyp, sigmoid neoplasm, epithelial tumor of colon

Subtypes (9): descending colon cancer, sigmoid colon cancer, colon carcinoma, cecum cancer, colon lymphoma, ascending colon cancer, transverse colon cancer, colon sarcoma, metastasis from malignant tumor of colon

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

32 retrieved; paginated sample, class counts are floors:

10 pathogenic, 7 uncertain significance, 6 conflicting classifications of pathogenicity, 6 pathogenic/likely pathogenic, 1 benign/likely benign, 1 benign, 1 no classifications from unflagged records

ClinVarVariant (HGVS)GeneClassificationReview
1210125NM_000051.4(ATM):c.3284+1G>TATMPathogenicno assertion criteria provided
17094NM_000249.4(MLH1):c.350C>T (p.Thr117Met)MLH1Pathogenicreviewed by expert panel
17098NM_000249.4(MLH1):c.806C>G (p.Ser269Ter)MLH1Pathogenicreviewed by expert panel
427760NM_000249.4(MLH1):c.1336_1337del (p.Ser446fs)MLH1Pathogeniccriteria provided, multiple submitters, no conflicts
433851NM_000249.4(MLH1):c.374C>A (p.Ala125Glu)MLH1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
455398NM_000249.4(MLH1):c.1667+1G>AMLH1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
560011NM_000249.4(MLH1):c.497dup (p.Leu166fs)MLH1Pathogenicno assertion criteria provided
635950NC_000003.12:g.36993510_36999509delMLH1Pathogeniccriteria provided, single submitter
89857NM_000249.4(MLH1):c.1731G>A (p.Ser577=)MLH1Pathogenicreviewed by expert panel
90430NM_000249.4(MLH1):c.887T>G (p.Leu296Ter)MLH1Pathogenicreviewed by expert panel
637008NM_000251.3(MSH2):c.2382del (p.Pro795fs)MSH2Pathogenicno assertion criteria provided
90670NM_000251.3(MSH2):c.1457_1460del (p.Asn486fs)MSH2Pathogenicreviewed by expert panel
135992NM_001048174.2(MUTYH):c.849+3A>CMUTYHPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
141595NM_001048174.2(MUTYH):c.464G>A (p.Gly155Asp)MUTYHPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
5294NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp)MUTYHPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
560019NM_000535.7(PMS2):c.1053del (p.Leu351fs)PMS2Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
236647NM_000038.6(APC):c.757G>A (p.Gly253Ser)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
490226NM_000038.6(APC):c.1803G>C (p.Glu601Asp)APCConflicting classifications of pathogenicitycriteria provided, conflicting classifications
128060NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met)CHEK2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
89649NM_000249.4(MLH1):c.1141C>T (p.His381Tyr)MLH1Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
631268NM_000251.3(MSH2):c.605C>T (p.Pro202Leu)MSH2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
127960NM_005431.2(XRCC2):c.620A>G (p.Glu207Gly)XRCC2Conflicting classifications of pathogenicitycriteria provided, conflicting classifications
411414NM_000038.6(APC):c.5026_5028del (p.Arg1676del)APCUncertain significancecriteria provided, multiple submitters, no conflicts
559945NM_000038.6(APC):c.5478G>C (p.Lys1826Asn)APCUncertain significancecriteria provided, single submitter
559947NM_000038.6(APC):c.3716G>A (p.Arg1239Lys)APCUncertain significancecriteria provided, multiple submitters, no conflicts
559964NM_000038.6(APC):c.2986A>G (p.Ser996Gly)APCUncertain significancecriteria provided, single submitter
433865NM_000249.4(MLH1):c.1238_1239del (p.Thr413fs)MLH1no classifications from unflagged recordsno classifications from unflagged records
198306NM_138694.4(PKHD1):c.10036T>C (p.Cys3346Arg)PKHD1Uncertain significancecriteria provided, multiple submitters, no conflicts
91351NM_000535.7(PMS2):c.320G>A (p.Arg107Gln)PMS2Uncertain significancecriteria provided, multiple submitters, no conflicts
560020NM_006231.4(POLE):c.1396A>G (p.Thr466Ala)POLEUncertain significancecriteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 71 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Somatic driver evidence (intOGen + CIViC, cohort fanout)

GeneintOGen roleCancer typesCIViC
BRAFActBLCA,BRCA,CHOL,CLLSLL,COAD,COADREAD,CSCC,DLBCLNOS,GBM,GIST,HGGNOS,LGGNOS,LUAD,MEL,MLYM,NSCLC,OVT,PAST,PCM,PRAD,PRCC,PROSTATE,READ,SACA,SKCM,STAD,UCEC,WDTCCIViC #5
ZEB1ActGBM,LUAD,LUSC,NPC,PCM,SCLCCIViC #5649
BIRC7CIViC #14842
ERBB2ActBLCA,BRCA,CESC,CHOL,COADREAD,EGC,ESCA,ESCC,LMS,LUAD,NSCLC,OVT,PRCC,READ,STAD,UCECCIViC #20
KRASActALL,AML,ANSC,BLADDER,BLCA,BRCA,CEAD,CESC,CHOL,CLLSLL,COAD,COADREAD,DLBCLNOS,EGC,ESCA,ESCC,HCC,LUAD,LUSC,MEL,MGCT,MT,NSCLC,OVT,PAAD,PANCREAS,PAST,PCM,PRAD,PRCC,READ,STAD,STOMACH,UCEC,UCS,WDTCCIViC #30
POU5F1CIViC #4419
CHEK2ActBRCACIViC #8950
CDH1LoFBLCA,BRCA,CSCC,DLBCLNOS,ESCA,STADCIViC #888
APCLoFAML,ANSC,CHOL,COAD,COADREAD,CSCC,EGC,ESCA,ESCC,HCC,LUAD,MEL,MT,NETNOS,NSCLC,PRAD,PROSTATE,READ,STAD,STOMACH,UM,VULVACIViC #66
MLH1CIViC #3532
MSH2CIViC #3628
ATMLoFBLCA,BRCA,CCRCC,CHOL,CLLSLL,COAD,COADREAD,ESCA,HCC,LUAD,LUSC,MEL,NSCLC,PAAD,PANCREAS,PANET,PCM,PLMESO,PRAD,PROSTATE,STAD,UCEC,UTUC,WDTCCIViC #69
PMS2ambiguousHCCCIViC #4371
POLD1LoFBRCA,ESCACIViC #4384
POLEActACC,BLCACIViC #4386

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
BRAFOrphanet:1340Cardiofaciocutaneous syndrome
BRAFOrphanet:146Differentiated thyroid carcinoma
BRAFOrphanet:251615Pilomyxoid astrocytoma
BRAFOrphanet:389Langerhans cell histiocytosis
BRAFOrphanet:500Noonan syndrome with multiple lentigines
BRAFOrphanet:54595Craniopharyngioma
BRAFOrphanet:58017Classic hairy cell leukemia
BRAFOrphanet:626Large/giant congenital melanocytic nevus
BRAFOrphanet:648Noonan syndrome
BRAFOrphanet:840Syringocystadenoma papilliferum
BRAFOrphanet:96253Cushing disease
ZEB1Orphanet:98973Posterior polymorphous corneal dystrophy
ZEB1Orphanet:98974Fuchs endothelial corneal dystrophy
ERBB2Orphanet:213726Serous carcinoma of the corpus uteri
ERBB2Orphanet:2800Extramammary Paget disease
ERBB2Orphanet:388Hirschsprung disease
ERBB2Orphanet:99976Adenocarcinoma of the oesophagus and oesophagogastric junction
KRASOrphanet:1333Familial pancreatic carcinoma
KRASOrphanet:1340Cardiofaciocutaneous syndrome
KRASOrphanet:144Lynch syndrome
KRASOrphanet:146Differentiated thyroid carcinoma
KRASOrphanet:2396Encephalocraniocutaneous lipomatosis
KRASOrphanet:251615Pilomyxoid astrocytoma
KRASOrphanet:2612Linear nevus sebaceus syndrome
KRASOrphanet:268114RAS-associated autoimmune leukoproliferative disease
KRASOrphanet:3339Oculoectodermal syndrome
KRASOrphanet:648Noonan syndrome
KRASOrphanet:86834Juvenile myelomonocytic leukemia
XRCC2Orphanet:227535Hereditary breast cancer
XRCC2Orphanet:399805Male infertility with azoospermia or oligozoospermia due to single gene mutation
XRCC2Orphanet:84Fanconi anemia
CHEK2Orphanet:1331Familial prostate cancer
CHEK2Orphanet:145Hereditary breast and/or ovarian cancer syndrome
CHEK2Orphanet:440437Familial colorectal cancer Type X
CHEK2Orphanet:524Li-Fraumeni syndrome
CHEK2Orphanet:668Osteosarcoma
CDH1Orphanet:1331Familial prostate cancer
CDH1Orphanet:199306Cleft lip/palate
CDH1Orphanet:1997Blepharo-cheilo-odontic syndrome
CDH1Orphanet:227535Hereditary breast cancer
CDH1Orphanet:26106Hereditary diffuse gastric cancer
APCOrphanet:220460Attenuated familial adenomatous polyposis
APCOrphanet:2615845q22 microdeletion syndrome
APCOrphanet:314022Gastric adenocarcinoma and proximal polyposis of the stomach
APCOrphanet:3258Cenani-Lenz syndrome
APCOrphanet:873Desmoid tumor
MLH1Orphanet:144Lynch syndrome
MLH1Orphanet:252202Constitutional mismatch repair deficiency syndrome
MSH2Orphanet:144Lynch syndrome
MSH2Orphanet:252202Constitutional mismatch repair deficiency syndrome

Cohort genes → proteins

18 cohort genes, 18 distinct canonical proteins.

Evidence partition

SubsetGenes
civic_only6
multi_evidence12

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
BRAFHGNC:1097ENSG00000157764P15056Serine/threonine-protein kinase B-rafcivic_evidence
ZEB1HGNC:11642ENSG00000148516P37275Zinc finger E-box-binding homeobox 1civic_evidence
BIRC7HGNC:13702ENSG00000101197Q96CA5Baculoviral IAP repeat-containing protein 7civic_evidence
ERBB2HGNC:3430ENSG00000141736P04626Receptor tyrosine-protein kinase erbB-2civic_evidence
KRASHGNC:6407ENSG00000133703P01116GTPase KRascivic_evidence
POU5F1HGNC:9221ENSG00000204531Q01860POU domain, class 5, transcription factor 1civic_evidence
XRCC2HGNC:12829ENSG00000196584O43543DNA repair protein XRCC2clinvar
CHEK2HGNC:16627ENSG00000183765O96017Serine/threonine-protein kinase Chk2clinvar
CDH1HGNC:1748ENSG00000039068P12830Cadherin-1clinvar
APCHGNC:583ENSG00000134982P25054Adenomatous polyposis coli proteinclinvar
MLH1HGNC:7127ENSG00000076242P40692DNA mismatch repair protein Mlh1clinvar
MSH2HGNC:7325ENSG00000095002P43246DNA mismatch repair protein Msh2clinvar
MUTYHHGNC:7527ENSG00000132781Q9UIF7Adenine DNA glycosylaseclinvar
ATMHGNC:795ENSG00000149311Q13315Serine-protein kinase ATMclinvar
PKHD1HGNC:9016ENSG00000170927P08F94Fibrocystinclinvar
PMS2HGNC:9122ENSG00000122512P54278Mismatch repair endonuclease PMS2clinvar
POLD1HGNC:9175ENSG00000062822P28340DNA polymerase delta catalytic subunitclinvar
POLEHGNC:9177ENSG00000177084Q07864DNA polymerase epsilon catalytic subunit Aclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
BRAFSerine/threonine-protein kinase B-rafProtein kinase involved in the transduction of mitogenic signals from the cell membrane to the nucleus.
ZEB1Zinc finger E-box-binding homeobox 1Acts as a transcriptional repressor.
BIRC7Baculoviral IAP repeat-containing protein 7Apoptotic regulator capable of exerting proapoptotic and anti-apoptotic activities and plays crucial roles in apoptosis, cell proliferation, and cell cycle control.
ERBB2Receptor tyrosine-protein kinase erbB-2Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding.
KRASGTPase KRasRas proteins bind GDP/GTP and possess intrinsic GTPase activity.
POU5F1POU domain, class 5, transcription factor 1Transcription factor that binds to the octamer motif (5’-ATTTGCAT-3’).
XRCC2DNA repair protein XRCC2Involved in the homologous recombination repair (HRR) pathway of double-stranded DNA, thought to repair chromosomal fragmentation, translocations and deletions.
CHEK2Serine/threonine-protein kinase Chk2Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest, activation of DNA repair and apoptosis in response to the presence of DNA double-strand breaks.
CDH1Cadherin-1Cadherins are calcium-dependent cell adhesion proteins.
APCAdenomatous polyposis coli proteinTumor suppressor.
MLH1DNA mismatch repair protein Mlh1Heterodimerizes with PMS2 to form MutL alpha, a component of the post-replicative DNA mismatch repair system (MMR).
MSH2DNA mismatch repair protein Msh2Component of the post-replicative DNA mismatch repair system (MMR).
MUTYHAdenine DNA glycosylaseInvolved in oxidative DNA damage repair.
ATMSerine-protein kinase ATMSerine/threonine protein kinase which activates checkpoint signaling upon double strand breaks (DSBs), apoptosis and genotoxic stresses such as ionizing ultraviolet A light (UVA), thereby acting as a DNA damage sensor.
PKHD1FibrocystinPromotes ciliogenesis in renal epithelial cells and therefore participates in the tubules formation and/ or ensures the maintenance of the architecture of the lumen of the kidney.
PMS2Mismatch repair endonuclease PMS2Component of the post-replicative DNA mismatch repair system (MMR).
POLD1DNA polymerase delta catalytic subunitAs the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair.
POLEDNA polymerase epsilon catalytic subunit ACatalytic component of the DNA polymerase epsilon complex.

Protein-family classification

Druggable: 6 · Difficult: 5 · Unknown: 7 · Druggable fraction: 0.33

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
Kinase46.2×0.017
Transcription factor52.3×0.144
Antibody/Immunoglobulin11.6×0.777
Other/Unknown70.7×0.954
Enzyme (other)10.7×0.954

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
BRAFKinaseyes2.7.10.2Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, PKC_DAG/PE
ZEB1Transcription factornoHD, Di19_Zn-bd, Homeodomain-like_sf
BIRC7Transcription factornoBIR_rpt, Znf_RING, Znf_RING/FYVE/PHD
ERBB2Kinaseyes2.7.10.1Rcpt_L-dom, Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom
KRASEnzyme (other)yes3.6.5.2Small_GTPase, Small_GTP-bd, Small_GTPase_Ras-type
POU5F1Transcription factornoPOU_dom, HD, Homeodomain-like_sf
XRCC2Other/UnknownnoRad51_C, RecA_ATP-bd, P-loop_NTPase
CHEK2Kinaseyes2.7.11.1FHA_dom, Prot_kinase_dom, Ser/Thr_kinase_AS
CDH1Other/UnknownnoCadherin_Y-type_LIR, Cadherin-like_dom, Cadherin_pro_dom
APCOther/UnknownnoArmadillo, APC_rpt, SAMP
MLH1Other/UnknownnoMutL/Mlh/PMS, DNA_mismatch_S5_2-like, Ribsml_uS5_D2-typ_fold_subgr
MSH2Other/UnknownnoDNA_mismatch_repair_MutS_C, DNA_mismatch_repair_MutS-lik_N, DNA_mismatch_repair_MutS_core
MUTYHOther/UnknownnoNUDIX_hydrolase_dom, HhH_motif, HhH-GPD_domain
ATMKinaseyes2.7.11.1PI3/4_kinase_cat_dom, PIK-rel_kinase_FAT, FATC_dom
PKHD1Antibody/ImmunoglobulinyesIPT_dom, PbH1, Pectin_lyase_fold/virulence
PMS2Other/UnknownnoMutL/Mlh/PMS, DNA_mismatch_S5_2-like, Ribsml_uS5_D2-typ_fold_subgr
POLD1Transcription factorno2.7.7.7DNA-dir_DNA_pol_B_exonuc, DNA-dir_DNA_pol_B_multi_dom, DNA-dir_DNA_pol_B
POLETranscription factorno2.7.7.7DNA-dir_DNA_pol_B_exonuc, DNA-dir_DNA_pol_B, RNaseH-like_sf

Expression context

Cohort genes with no expression data: 0.

18 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)0
broad (>20)18
unknown0

Top tissues across cohort

TissueCohort genes
calcaneal tendon3
colonic epithelium3
primordial germ cell in gonad3
buccal mucosa cell2
sural nerve2
lower esophagus mucosa2
right uterine tube2
metanephros cortex2
male germ line stem cell (sensu Vertebrata) in testis2
ventricular zone2
cerebellar hemisphere2
right hemisphere of cerebellum2
tendon1
adrenal tissue1
tibial nerve1
nipple1
pylorus1
trigeminal ganglion1
lateral globus pallidus1
tendon of biceps brachii1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
BRAF265ubiquitousmarkerbuccal mucosa cell, colonic epithelium, calcaneal tendon
ZEB1287ubiquitousmarkercalcaneal tendon, colonic epithelium, tendon
BIRC7109tissue_specificmarkeradrenal tissue, tibial nerve, sural nerve
ERBB2276ubiquitousmarkerlower esophagus mucosa, right uterine tube, sural nerve
KRAS298ubiquitousmarkertrigeminal ganglion, pylorus, nipple
POU5F1132tissue_specificmarkerprimordial germ cell in gonad, right uterine tube, metanephros cortex
XRCC2283ubiquitousmarkerbuccal mucosa cell, tendon of biceps brachii, lateral globus pallidus
CHEK2183ubiquitousmarkerprimordial germ cell in gonad, lower esophagus mucosa, male germ line stem cell (sensu Vertebrata) in testis
CDH1245broadmarkerjejunal mucosa, esophagus squamous epithelium, gingival epithelium
APC297ubiquitousmarkersubstantia nigra pars compacta, substantia nigra pars reticulata, medial globus pallidus
MLH1296ubiquitousmarkertibialis anterior, skeletal muscle tissue of rectus abdominis, deltoid
MSH2278ubiquitousmarkersecondary oocyte, oocyte, ventricular zone
MUTYH134ubiquitousmarkercerebellar hemisphere, cerebellar cortex, right hemisphere of cerebellum
ATM286ubiquitousmarkercalcaneal tendon, colonic epithelium, corpus callosum
PKHD151tissue_specificmarkerkidney epithelium, renal medulla, metanephros cortex
PMS2143ubiquitousmarkerthymus, prefrontal cortex, male germ line stem cell (sensu Vertebrata) in testis
POLD1134ubiquitousmarkermucosa of transverse colon, ventricular zone, primordial germ cell in gonad
POLE221ubiquitousmarkerright hemisphere of cerebellum, right testis, cerebellar hemisphere

Protein interactions among cohort

Intra-cohort edges: 28.

Hub genes (top 10 by interactor count)

SymbolInteractor count
KRAS14,509
ERBB29,659
CDH18,738
BRAF7,394
ATM7,383
CHEK24,795
MSH24,537
MLH14,435
ZEB14,171
POLD14,000

Intra-cohort edges

ABSources
ATMCHEK2string_interaction
ATMMLH1string_interaction
ATMMSH2string_interaction
ATMZEB1biogrid_interaction
BRAFKRASbiogrid_interaction, intact, string_interaction
BRAFMLH1string_interaction
BRAFPMS2string_interaction
BRAFPOLEintact
CDH1ERBB2string_interaction
CDH1ZEB1string_interaction
CHEK2XRCC2string_interaction
ERBB2KRASstring_interaction
MLH1MSH2string_interaction
MLH1MUTYHstring_interaction
MLH1PMS2biogrid_interaction, intact, string_interaction
MLH1POLD1string_interaction
MLH1POLEstring_interaction
MSH2MUTYHintact, string_interaction
MSH2PMS2string_interaction
MSH2POLD1string_interaction
MSH2POLEstring_interaction
MUTYHPMS2string_interaction
MUTYHPOLD1string_interaction
MUTYHPOLEstring_interaction
PMS2POLD1string_interaction
PMS2POLEstring_interaction
PMS2XRCC2string_interaction
POLD1POLEstring_interaction

Structural data

PDB: 17 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
KRASP01116511
BRAFP15056131
ERBB2P0462663
CHEK2O9601738
APCP2505431
MSH2P4324630
CDH1P1283022
POLEQ0786418
POU5F1Q0186016
XRCC2O4354316
ATMQ1331514
BIRC7Q96CA513
PMS2P542789
MLH1P406927
POLD1P283406
MUTYHQ9UIF73
ZEB1P372751

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
PKHD1P08F94

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 291. Enrichment computed across 18 evidence-associated genes (17 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 17 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)4191.9×5e-07MLH1, MSH2, PMS2, POLD1
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)4191.9×5e-07MLH1, MSH2, PMS2, POLD1
Defective Mismatch Repair Associated With MLH12671.8×1e-04MLH1, PMS2
Defective Mismatch Repair Associated With PMS22671.8×1e-04MLH1, PMS2
HDR through Homologous Recombination (HRR)444.8×1e-04XRCC2, ATM, POLD1, POLE
TP53 Regulates Transcription of DNA Repair Genes442.6×1e-04MLH1, MSH2, ATM, PMS2
Diseases of DNA repair3100.8×1e-04MLH1, MSH2, ATM
Mismatch Repair2335.9×4e-04MLH1, MSH2
Diseases of Mismatch Repair (MMR)2335.9×4e-04MLH1, MSH2
Constitutive Signaling by Overexpressed ERBB22112.0×0.004ERBB2, KRAS
Regulation of MITF-M-dependent genes involved in extracellular matrix, focal adhesion and epithelial-to-mesenchymal transition2103.3×0.004ZEB1, CDH1
Stabilization of p53289.6×0.005CHEK2, ATM
Developmental Lineage of Mammary Stem Cells289.6×0.005CDH1, ERBB2
Signaling by ERBB2 ECD mutants279.0×0.006ERBB2, KRAS
GRB2 events in ERBB2 signaling274.6×0.006ERBB2, KRAS
Regulation of TP53 Activity through Methylation264.0×0.007CHEK2, ATM
Developmental Lineage of Mammary Gland Myoepithelial Cells264.0×0.007CDH1, ERBB2
PCNA-Dependent Long Patch Base Excision Repair261.1×0.007POLD1, POLE
Apoptotic cleavage of cellular proteins256.0×0.007CDH1, APC
SHC1 events in ERBB2 signaling256.0×0.007ERBB2, KRAS
Apoptotic execution phase256.0×0.007CDH1, APC
Signaling by ERBB2 TMD/JMD mutants256.0×0.007ERBB2, KRAS
Impaired BRCA2 binding to PALB2253.7×0.007XRCC2, ATM
Developmental Lineage of Mammary Gland Luminal Epithelial Cells253.7×0.007CDH1, ERBB2
Gap-filling DNA repair synthesis and ligation in GG-NER251.7×0.007POLD1, POLE
Signaling by ERBB2 KD Mutants249.8×0.007ERBB2, KRAS
Defective homologous recombination repair (HRR) due to BRCA1 loss of function249.8×0.007XRCC2, ATM
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function249.8×0.007XRCC2, ATM
Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function249.8×0.007XRCC2, ATM
DNA Repair317.4×0.007MLH1, MSH2, ATM

GO biological processes 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.

GO termCohort genesFoldFDRSample cohort genes
positive regulation of isotype switching to IgA isotypes3468.1×4e-06MLH1, MSH2, PMS2
mismatch repair4144.0×4e-06MLH1, MSH2, MUTYH, PMS2
positive regulation of isotype switching to IgG isotypes3255.3×2e-05MLH1, MSH2, PMS2
somatic hypermutation of immunoglobulin genes3175.5×5e-05MLH1, MSH2, PMS2
DNA replication proofreading2624.1×2e-04POLD1, POLE
somatic recombination of immunoglobulin gene segments2468.1×4e-04MSH2, PMS2
nucleotide-excision repair, DNA gap filling2312.1×8e-04POLD1, POLE
negative regulation of neuron apoptotic process424.6×8e-04BRAF, XRCC2, KRAS, MSH2
intrinsic apoptotic signaling pathway in response to DNA damage354.0×8e-04CHEK2, MLH1, ATM
regulation of microtubule-based process2208.1×0.001ERBB2, APC
meiotic telomere clustering2208.1×0.001MLH1, ATM
double-strand break repair333.8×0.003CHEK2, MSH2, ATM
base-excision repair, gap-filling2124.8×0.003POLD1, POLE
regulation of autophagosome assembly2124.8×0.003CHEK2, ATM
protein phosphorylation415.1×0.003BRAF, CHEK2, ERBB2, ATM
replicative senescence2110.1×0.003CHEK2, ATM
DNA synthesis involved in DNA repair2104.0×0.003POLD1, POLE
mitotic intra-S DNA damage checkpoint signaling2104.0×0.003CHEK2, MSH2
DNA repair414.2×0.003XRCC2, MSH2, MUTYH, POLD1
response to X-ray298.5×0.003XRCC2, MSH2
cellular response to stress293.6×0.003CHEK2, ATM
isotype switching293.6×0.003MLH1, MSH2
signal transduction in response to DNA damage289.2×0.003CHEK2, ATM
cellular response to gamma radiation266.9×0.006CHEK2, ATM
regulation of ERK1 and ERK2 cascade264.6×0.006ERBB2, PKHD1
DNA-templated DNA replication262.4×0.006POLD1, POLE
mitotic spindle assembly checkpoint signaling262.4×0.006APC, ATM
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator255.1×0.007CHEK2, MSH2
pattern specification process252.0×0.008ZEB1, APC
determination of adult lifespan248.0×0.009MSH2, ATM

Therapeutics

Drug target analysis

Approved (phase 4): 6 · Phase ≥3: 6 · Phased (≥1): 7 · Undrugged: 11

Druggability breadth: 14 of 18 evidence-associated genes (78%) 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
BRAFVEMURAFENIB
ERBB2CLOTRIMAZOLE
KRASVEMURAFENIB
POU5F1FAMOTIDINE
CHEK2NERATINIB
ATMAMIODARONE HYDROCHLORIDE

Top cohort targets by molecule count

SymbolMoleculesMax phase
ERBB2834
BRAF484
ATM354
CHEK2304
KRAS114
BIRC732
POU5F114
ZEB100
XRCC200
CDH100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
VEMURAFENIB4BRAF, KRAS
PONATINIB4BRAF, ERBB2
FEDRATINIB4BRAF
SORAFENIB4BRAF, ERBB2
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF
INFIGRATINIB4BRAF
REGORAFENIB4BRAF
DABRAFENIB4BRAF, KRAS
COBIMETINIB4BRAF
NILOTINIB4BRAF
ABEMACICLIB4BRAF
ENCORAFENIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF
DASATINIB4BRAF, ERBB2
ERLOTINIB4BRAF, ERBB2
GEFITINIB4BRAF, CHEK2, ERBB2
IMATINIB4BRAF, ERBB2
CLOTRIMAZOLE4ERBB2
ERLOTINIB HYDROCHLORIDE4ERBB2
AFATINIB4ERBB2
LAPATINIB DITOSYLATE4ERBB2
NERATINIB4CHEK2, ERBB2
IBRUTINIB4ERBB2
AFATINIB DIMALEATE4ERBB2
CABOZANTINIB4ERBB2
DACOMITINIB4ERBB2
DACOMITINIB ANHYDROUS4ERBB2

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 7.

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

SymbolAssaysType breakdown
BRAF1,442Binding:1400, Functional:37, ADMET:5
ERBB21,221Binding:1136, Functional:79, ADMET:6
KRAS861Binding:829, Functional:32
CHEK2690Binding:687, Functional:2, ADMET:1
ATM240Binding:233, Functional:5, ADMET:2
POU5F136Binding:36
APC24Binding:24
CDH118Binding:18
BIRC714Binding:13, Functional:1
MSH29Binding:9
POLD18Binding:8
MUTYH1Functional:1
PMS21Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
BRAF2.7.10.2, 2.7.11.1non-specific protein-tyrosine kinase, non-specific serine/threonine protein kinase
ERBB22.7.10.1receptor protein-tyrosine kinase
KRAS3.6.5.2small monomeric GTPase
CHEK22.7.11.1non-specific serine/threonine protein kinase
ATM2.7.11.1non-specific serine/threonine protein kinase
POLD12.7.7.7DNA-directed DNA polymerase
POLE2.7.7.7DNA-directed DNA polymerase

Cohort genes with high screening signal

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

SymbolChEMBL assays
BRAF1,442
ERBB21,221
KRAS861
CHEK2690
ATM240

Pharmacogenomics

Cohort genes with a PharmGKB record: 18; with CPIC/DPWG dosing guidelines: 0.

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

Drug repurposing candidates

27 approved/phased drugs hit cohort targets but don’t yet appear in disease-level clinical trials. Target-inhibition rationale is strongest for cancer driver genes; a bioactivity hit is a screening signal, not a treatment claim.

CompoundMax phaseCohort target (bioactivity)
VEMURAFENIB4BRAF, KRAS
PONATINIB4BRAF, ERBB2
FEDRATINIB4BRAF
SORAFENIB4BRAF, ERBB2
DASATINIB ANHYDROUS4BRAF
RUXOLITINIB4BRAF
INFIGRATINIB PHOSPHATE4BRAF
INFIGRATINIB4BRAF
REGORAFENIB4BRAF
DABRAFENIB4BRAF, KRAS
COBIMETINIB4BRAF
NILOTINIB4BRAF
TOVORAFENIB4BRAF
PAZOPANIB4BRAF
DASATINIB4BRAF, ERBB2
ERLOTINIB4BRAF, ERBB2
GEFITINIB4BRAF, CHEK2, ERBB2
IMATINIB4BRAF, ERBB2
CLOTRIMAZOLE4ERBB2
AFATINIB4ERBB2
LAPATINIB DITOSYLATE4ERBB2
NERATINIB4CHEK2, ERBB2
IBRUTINIB4ERBB2
AFATINIB DIMALEATE4ERBB2
CABOZANTINIB4ERBB2
DACOMITINIB4ERBB2
DACOMITINIB ANHYDROUS4ERBB2

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)6BRAF, ERBB2, KRAS, POU5F1, CHEK2, ATM
BPhased (≥1) drug, not yet approved1BIRC7
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug1PKHD1
EDifficult family or no structure, no drug10ZEB1, XRCC2, CDH1, APC, MLH1, MSH2, MUTYH, PMS2, POLD1, POLE

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
ZEB10
XRCC20
CDH118
APC24
MLH10
MSH29
MUTYH1
PKHD10
PMS21
POLD18
POLE0

Clinical trials & evidence

Clinical trials

Clinical trials: 1,079.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified599
PHASE2174
PHASE1120
PHASE376
PHASE1/PHASE272
PHASE415
EARLY_PHASE112
PHASE2/PHASE311

Top trials by phase / activity

NCTPhaseStatusTitle
NCT05250648PHASE4RECRUITINGClinical Trial on HIPEC With Mitomycin C in Colon Cancer Peritoneal Metastases (GECOP-MMC)
NCT01169220PHASE4COMPLETEDBowel Preparation for Inpatient Colonoscopy
NCT01170754PHASE4COMPLETEDMiralax (PEG 3350) vs. Golytely as Bowel Preparation for Screening Colonoscopy
NCT02052557PHASE4COMPLETEDThe Effect of Exparel on Post Operative Pain and Narcotic Use After Colon Surgery
NCT02078726PHASE4COMPLETEDGlucagon Use in Colonoscopies
NCT02231203PHASE4COMPLETEDEffect of Omega-3 Fatty Acids on the Perioperative Immune Response and Erythrocyte Function
NCT02314871PHASE4COMPLETEDEffects of Different Types of Perioperative Analgesia on Minimal Residual Disease Development After Colon Cancer Surgery
NCT02746432PHASE4UNKNOWNInsulin Therapy Reduce Post-Operative Inflammatory Response After Curative Colorectal Cancer Resection: Randomization Controlled Trial
NCT02887365PHASE4UNKNOWNA Phase II Study of Tegafur-Uracil as Maintenance Chemotherapy in Patients With Stage II of Colon Cancer
NCT02937506PHASE4COMPLETEDPatient Satisfaction With Propofol for Out Patient Colonoscopy
NCT02958566PHASE4UNKNOWNMultimodal Narcotic Limited Perioperative Pain Control With Colorectal Surgery
NCT03980704PHASE4COMPLETEDPreoperative High Protein vs Immunodiet in Surgical Cancer Patients
NCT04269369PHASE4UNKNOWNImplementation of Pre-emptive Geno- and Phenotyping in 5-Fluorouracil- or Capecitabine-treated Patients
NCT04311099PHASE4COMPLETEDOptimal Peripheral Nerve Block After Minimally Invasive Colon Surgery
NCT04709770PHASE4UNKNOWNLow-volume vs High-volume Polyethylene Glycol Based Bowel Preparation for Colonoscopy in People Receiving Hemodialysis
NCT00217737PHASE3ACTIVE_NOT_RECRUITINGOxaliplatin, Leucovorin, and Fluorouracil With or Without Bevacizumab in Treating Patients Who Have Undergone Surgery for Stage II Colon Cancer
NCT01460589PHASE3ACTIVE_NOT_RECRUITINGEarly Commencement of Adjuvant Chemotherapy for Colon Cancer
NCT01918527PHASE3ACTIVE_NOT_RECRUITINGNeoadjuvant Chemotherapy Versus Standard Treatment in Patients With Locally Advanced Colon Cancer
NCT02301286PHASE3ACTIVE_NOT_RECRUITINGA Trial of Aspirin on Recurrence and Survival in Colon Cancer Patients
NCT02448173PHASE3NOT_YET_RECRUITINGA Multicenter Study of Active Specific Immunotherapy With OncoVax® in Patients With Stage II Colon Cancer
NCT02572141PHASE3ACTIVE_NOT_RECRUITINGFOLFOX or CAPOX Perioperative Chemotherapy Versus Postoperative Chemotherapy for Locally Advanced Colon Cancer (OPTICAL)
NCT02912559PHASE3ACTIVE_NOT_RECRUITINGCombination Chemotherapy With or Without Atezolizumab in Treating Patients With Stage III Colon Cancer and Deficient DNA Mismatch Repair
NCT03125980PHASE3RECRUITINGPerioperative Versus Postoperative CapOX Chemotherapy for Locally Advanced Colon Cancer
NCT03426904PHASE3ACTIVE_NOT_RECRUITINGNeoadjuvant FOLFOX Chemotherapy for Patients With Locally Advanced Colon Cancer
NCT03428477PHASE3ACTIVE_NOT_RECRUITINGEPA for Metastasis Trial 2
NCT03464305PHASE3ACTIVE_NOT_RECRUITINGASPIRIN Trial Belgium
NCT03803553PHASE3RECRUITINGIdentification and Treatment Of Micrometastatic Disease in Stage III Colon Cancer
NCT04068103PHASE2/PHASE3ACTIVE_NOT_RECRUITINGCirculating Tumor DNA Testing in Predicting Treatment for Patients With Stage IIA Colon Cancer After Surgery
NCT04089631PHASE3RECRUITINGCirculating Tumour DNA Based Decision for Adjuvant Treatment in Colon Cancer Stage II Evaluation
NCT05174169PHASE2/PHASE3RECRUITINGColon Adjuvant Chemotherapy Based on Evaluation of Residual Disease
NCT05179889PHASE2/PHASE3RECRUITINGAdjuvant mFOLFIRINOX for High-risk Stage III Colon Cancer
NCT05194878PHASE3RECRUITINGNeoadjuvant FOLFOXIRI Versus Immediate Surgery for Stage II and III Colon Cancers
NCT05534087PHASE3RECRUITINGPlatform Study of Circulating Tumor DNA Directed Adjuvant Chemotherapy in Colon Cancer (KCSG CO22-12)
NCT05709249PHASE3RECRUITINGXian-Lian-Jie-Du Optimization Decoction As an Adjuvant Treatment for Prevention of Recurrence of Colon Cancer
NCT05710406PHASE2/PHASE3ACTIVE_NOT_RECRUITINGTesting the Use of BRAF-Targeted Therapy After Surgery and Usual Chemotherapy for BRAF-Mutated Colon Cancer
NCT06107920PHASE3RECRUITINGNeoadjuvant Chemotherapy for Obstructive Colon cancER First Treated by cOlostomy
NCT06293625PHASE3RECRUITINGPersonalising and Refining Neo-adjuvant Chemotherapy in Locally Advanced but Resecable Colon Cancer in the Elderly of 70 Years Old or More
NCT06446557PHASE3NOT_YET_RECRUITINGDe-scalation or swItch of Treatment According to Circulating tuMOr DNA Variation After 2 Cycles of Doublet Chemotherapy Plus Targeted Agent in Metastatic Unresectable Colorectal Cancer
NCT06490536PHASE3RECRUITINGThe Sagittarius Trial
NCT06609551PHASE3RECRUITINGctDNA-guided Selection of Adjuvant Chemotherapy Regimens for Elderly Colon Cancer Patients After Surgery: A Single-center, Randomized, Controlled Study

Drugs tested across these trials (top 30)

MoleculeMax phaseTrials referencing
LEUCOVORIN424
PANITUMUMAB49
TIPIRACIL49
OXALIPLATIN48
TRIFLURIDINE47
ASPIRIN46
BEVACIZUMAB45
ENCORAFENIB45
FLUOROURACIL45
IRINOTECAN HYDROCHLORIDE45
FLOXURIDINE44
FRUQUINTINIB44
CEMIPLIMAB43
CETUXIMAB43
MORPHINE43
PERTUZUMAB43
SELUMETINIB43
BINIMETINIB42
BUPIVACAINE42
DOSTARLIMAB42
ERLOTINIB HYDROCHLORIDE42
PEGFILGRASTIM42
POLYETHYLENE GLYCOL 335042
RALTITREXED42
SELPERCATINIB42
TEGAFUR42
TUCATINIB42
ABEMACICLIB41
ATEZOLIZUMAB41
ATORVASTATIN CALCIUM41

Precision-medicine subtype map (CIViC)

Drug × molecular subtype: 21 predictive associations from 21 curated evidence items; also 1 oncogenic, 1 prognostic.

Molecular subtypeTherapyEffectLevelCIViC
KRAS G13DCetuximabSensitivity/ResponseCIViC BEID6974
KRAS G12ACetuximabResistanceCIViC CEID3717
KRAS G12CCetuximabResistanceCIViC CEID3981
KRAS G12DCetuximabResistanceCIViC CEID3960
KRAS G12RCetuximabResistanceCIViC CEID3998
KRAS G12VCetuximabResistanceCIViC CEID3931
KRAS G13DCetuximabResistanceCIViC CEID3896
BRAF V600ERegorafenib AnhydrousSensitivity/ResponseCIViC DEID3776
ERBB2 L755SLapatinib + Neratinib + TrastuzumabSensitivity/ResponseCIViC DEID1176
ERBB2 L866MTrastuzumab + Neratinib + LapatinibSensitivity/ResponseCIViC DEID1178
ERBB2 S310F/YNeratinib + Trastuzumab + LapatinibSensitivity/ResponseCIViC DEID1179
ERBB2 V777LLapatinib + Trastuzumab + NeratinibSensitivity/ResponseCIViC DEID1177
ERBB2 V842ITrastuzumab + Lapatinib + NeratinibSensitivity/ResponseCIViC DEID1174
FGFR2 OverexpressionRogaratinibSensitivity/ResponseCIViC DEID7830
KRAS G12VRegorafenib AnhydrousSensitivity/ResponseCIViC DEID3932
KRAS G13DRegorafenib AnhydrousSensitivity/ResponseCIViC DEID3897
BIRC7 AmplificationCisplatinResistanceCIViC DEID661
CIC LossTrametinibResistanceCIViC DEID5111
CIC LossVemurafenibResistanceCIViC DEID5112
POU5F1 EXPRESSIONOxaliplatinResistanceCIViC DEID958
ZEB1 ExpressionOxaliplatinResistanceCIViC DEID8086