Adenomatous colon polyp

Summary

Adenomatous colon polyp (MONDO:0006498) is a disease with 1 cohort gene and 11 clinical trials. Top therapeutic interventions include diltiazem.

At a glance

• Cohort genes: 1
• ClinVar variants: 1
• Clinical trials: 11

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	adenomatous colon polyp
Mondo ID	MONDO:0006498
EFO	EFO:1000633
ICD-11	248829180
NCIT	C96479
SNOMED CT	428054006
UMLS	C0850572
MedGen	163407
Is cancer (heuristic)	no

Also known as: adenomatous polyp of colon · adenomatous polyp of the colon · colon adenomatous polyp · colonic adenomatous polyp

Data availability: 1 ClinVar variant · 1 HPO phenotype.

Disease family

Classification path: disease › human disease › disease by body system or component › digestive system disorder › intestinal disorder › intestinal neoplasm › colorectal neoplasm › colorectal adenoma › colon adenoma › adenomatous colon polyp

Related subtypes (3): appendix adenoma, colon sessile serrated adenoma/polyp, villous adenoma 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

1 retrieved; paginated sample, class counts are floors:

1 uncertain significance

ClinVar	Variant (HGVS)	Gene	Classification	Review
407970	NM_002691.4(POLD1):c.367C>T (p.Pro123Ser)	POLD1	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 0 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
POLD1	Orphanet:363649	Mandibular hypoplasia-deafness-progeroid features-lipodystrophy syndrome
POLD1	Orphanet:440437	Familial colorectal cancer Type X
POLD1	Orphanet:447877	Polymerase proofreading-related polyposis

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
POLD1	HGNC:9175	ENSG00000062822	P28340	DNA polymerase delta catalytic subunit	clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
POLD1	DNA polymerase delta catalytic subunit	As 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.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.0

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.

Family	Genes	Fold	FDR
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
POLD1	Transcription factor	no	2.7.7.7	DNA-dir_DNA_pol_B_exonuc, DNA-dir_DNA_pol_B_multi_dom, DNA-dir_DNA_pol_B

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
mucosa of transverse colon	1
primordial germ cell in gonad	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
POLD1	134	ubiquitous	marker	mucosa of transverse colon, ventricular zone, primordial germ cell in gonad

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
POLD1	4,000

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
POLD1	P28340	6

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 18. Enrichment computed across 1 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

Pathway	Cohort genes	Fold	FDR	Sample cohort genes
Processive synthesis on the lagging strand	1	1142.0×	0.003	POLD1
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)	1	815.7×	0.003	POLD1
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)	1	815.7×	0.003	POLD1
Polymerase switching	1	815.7×	0.003	POLD1
Removal of the Flap Intermediate	1	815.7×	0.003	POLD1
Processive synthesis on the C-strand of the telomere	1	761.3×	0.003	POLD1
Telomere C-strand (Lagging Strand) Synthesis	1	761.3×	0.003	POLD1
Cytosolic iron-sulfur cluster assembly	1	761.3×	0.003	POLD1
Removal of the Flap Intermediate from the C-strand	1	634.4×	0.003	POLD1
PCNA-Dependent Long Patch Base Excision Repair	1	519.1×	0.003	POLD1
Gap-filling DNA repair synthesis and ligation in GG-NER	1	439.2×	0.004	POLD1
Polymerase switching on the C-strand of the telomere	1	423.0×	0.004	POLD1
Recognition of DNA damage by PCNA-containing replication complex	1	380.7×	0.004	POLD1
Termination of translesion DNA synthesis	1	346.1×	0.004	POLD1
Dual Incision in GG-NER	1	259.6×	0.005	POLD1
HDR through Homologous Recombination (HRR)	1	190.3×	0.006	POLD1
Gap-filling DNA repair synthesis and ligation in TC-NER	1	178.4×	0.006	POLD1
Dual incision in TC-NER	1	173.0×	0.006	POLD1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
DNA replication proofreading	1	5617.3×	0.001	POLD1
error-free translesion synthesis	1	3370.4×	0.001	POLD1
nucleotide-excision repair, DNA gap filling	1	2808.7×	0.001	POLD1
base-excision repair, gap-filling	1	1123.5×	0.002	POLD1
DNA synthesis involved in DNA repair	1	936.2×	0.002	POLD1
fatty acid homeostasis	1	936.2×	0.002	POLD1
DNA biosynthetic process	1	802.5×	0.002	POLD1
DNA-templated DNA replication	1	561.7×	0.003	POLD1
response to UV	1	366.4×	0.004	POLD1
cellular response to UV	1	295.6×	0.004	POLD1
DNA replication	1	165.2×	0.007	POLD1
DNA repair	1	63.8×	0.016	POLD1

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
POLD1	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
POLD1	8	Binding:8

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
POLD1	2.7.7.7	DNA-directed DNA polymerase

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

0 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.

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	POLD1

Undrugged target profiles

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

Symbol	ChEMBL assays	Drugged partners (top 3)
POLD1	8	—

Clinical trials & evidence

Clinical trials

Clinical trials: 11.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	10
EARLY_PHASE1	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT04017845	EARLY_PHASE1	COMPLETED	Screening for Colorectal Cancer in Average and High Risk Population
NCT02051465	Not specified	COMPLETED	Effectiveness and Safety of the Endoscopic Removal of Large and Flat Colonic Polyps With LumenR RetractorTM
NCT02117232	Not specified	COMPLETED	Effectiveness and Safety of the Colonoscopy With Visualization Balloon
NCT02289053	Not specified	COMPLETED	Prevalence and Topography of Adenomas in 40-49 Year Old Patients With a Family History of Colon Cancer
NCT02538406	Not specified	TERMINATED	The Utility of Time Segmental Withdrawal During Screening Colonoscopy for Increasing Adenoma Detection Rate.
NCT02540850	Not specified	COMPLETED	CRC Screening Using mSEPT9 (Methylated Septin 9) in Chinese Population
NCT03942965	Not specified	UNKNOWN	Registry Evaluation of a Double Balloon Accessory Device
NCT04441242	Not specified	COMPLETED	Ambient Lighting During Colonoscopy and Its Effect on Adenoma Detection Rate and Eye Fatigue
NCT04551001	Not specified	COMPLETED	Evaluation of Cold Forcep and Cold Snare Polypectomy for Polyps Less Than or Equal to 3mm in Size During Colonoscopy
NCT04551014	Not specified	COMPLETED	Evaluation of EverLift in the Performance of Polypectomy for Polyps 4-9mm
NCT04607083	Not specified	COMPLETED	Impact of Computer-aided Optical Diagnosis (CAD) in Predicting Histology of Diminutive Rectosigmoid Polyps: a Multicenter Prospective Trial (ABC Study).

Drugs tested across these trials (top 30)

Molecule	Max phase	Trials referencing
DILTIAZEM	4	3