Gastric neuroendocrine neoplasm

Summary

Gastric neuroendocrine neoplasm (MONDO:0003111) is a cancer with 1 cohort gene.

At a glance

• Classification: Cancer
• Prevalence: 1-9 / 100 000 (Europe) [Orphanet-validated]
• Cohort genes: 1
• Phenotypes (HPO): 32

Clinical features

Epidemiology

Prevalence records

4 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Point prevalence	1-9 / 100 000	3.2	Europe	Validated
Point prevalence	1-9 / 100 000	1.7	United States	Validated
Point prevalence	1-9 / 1 000 000	0.7	United Kingdom	Validated
Point prevalence	1-9 / 1 000 000	0.5	Japan	Validated

Signs & symptoms

Clinical features (HPO)

32 HPO clinical features (Orphanet curated; top 32 by frequency):

HPO ID	Term	Frequency
HP:0100570	Carcinoid tumor	Obligate (100%)
HP:0001824	Weight loss	Frequent (30-79%)
HP:0001891	Iron deficiency anemia	Frequent (30-79%)
HP:0002017	Nausea and vomiting	Frequent (30-79%)
HP:0002039	Anorexia	Frequent (30-79%)
HP:0002254	Intermittent diarrhea	Frequent (30-79%)
HP:0002574	Episodic abdominal pain	Frequent (30-79%)
HP:0004396	Poor appetite	Frequent (30-79%)
HP:0001005	Dermatological manifestations of systemic disorders	Occasional (5-29%)
HP:0002044	Zollinger-Ellison syndrome	Occasional (5-29%)
HP:0002240	Hepatomegaly	Occasional (5-29%)
HP:0002248	Hematemesis	Occasional (5-29%)
HP:0002249	Melena	Occasional (5-29%)
HP:0002730	Chronic noninfectious lymphadenopathy	Occasional (5-29%)
HP:0002910	Elevated circulating hepatic transaminase concentration	Occasional (5-29%)
HP:0025085	Bloody diarrhea	Occasional (5-29%)
HP:0030145	Lack of bowel sounds	Occasional (5-29%)
HP:0030446	Atypical pulmonary carcinoid tumor	Occasional (5-29%)
HP:4000007	Bronchoconstriction	Very rare (<1-4%)
HP:0001399	Hepatic failure	Very rare (<1-4%)
HP:0001708	Right ventricular failure	Very rare (<1-4%)
HP:0001962	Palpitations	Very rare (<1-4%)
HP:0002615	Hypotension	Very rare (<1-4%)
HP:0002668	Paraganglioma	Very rare (<1-4%)
HP:0003144	Increased serum serotonin	Very rare (<1-4%)
HP:0003154	Increased circulating ACTH level	Very rare (<1-4%)
HP:0004385	Protracted diarrhea	Very rare (<1-4%)
HP:0005180	Tricuspid regurgitation	Very rare (<1-4%)
HP:0007380	Facial telangiectasia	Very rare (<1-4%)
HP:0012701	Bowel urgency	Very rare (<1-4%)
HP:0030149	Cardiogenic shock	Very rare (<1-4%)
HP:0031566	Abnormal pulmonary valve cusp morphology	Very rare (<1-4%)

Identifiers

Disease identifiers

Field	Value
Canonical name	gastric neuroendocrine neoplasm
Mondo ID	MONDO:0003111
Orphanet	100075
DOID	DOID:4715
NCIT	C5696
SNOMED CT	721194008
UMLS	C1333783
MedGen	232548
GARD	0019750
Anatomy (UBERON)	UBERON:0000945
Is cancer (heuristic)	yes

Also known as: gastric neuroendocrine neoplasm · NET of stomach · neuroendocrine neoplasm of stomach · neuroendocrine neoplasm of the stomach · neuroendocrine tumour of stomach · neuroendocrine tumour of the stomach · stomach NET · stomach neuroendocrine neoplasm · stomach neuroendocrine tumor · stomach neuroendocrine tumor, well differentiated, low or intermediate grade · stomach neuroendocrine tumour

Data availability: 1 GenCC gene-disease record.

Disease family

An umbrella term covering 2 Mondo subtypes.

Classification path: disease › human disease › disease by body system or component › digestive system disorder › stomach disorder › gastric neoplasm › gastric neuroendocrine neoplasm

Related subtypes (5): gastric cancer, gastric teratoma, gastric adenoma, gastric hamartomatous polyp, benign neoplasm of stomach

Subtypes (2): gastric small cell neuroendocrine carcinoma, gastric neuroendocrine tumor, well differentiated, low or intermediate grade

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

No tiered GWAS variants or ClinVar records for this disease.

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 2 · Orphanet: 1 · 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.

Gene	Classification	Inheritance	Disease	Records
ATP4A	Supportive	Autosomal recessive	familial gastric type 1 neuroendocrine tumor	2

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
ATP4A	Orphanet:464756	Familial gastric type 1 neuroendocrine tumor

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
ATP4A	HGNC:819	ENSG00000105675	P20648	Potassium-transporting ATPase alpha chain 1	gencc

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
ATP4A	Potassium-transporting ATPase alpha chain 1	The catalytic subunit of the gastric H(+)/K(+) ATPase pump which transports H(+) ions in exchange for K(+) ions across the apical membrane of parietal cells.

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)
ATP4A	Transcription factor	no	7.2.2.19	P_typ_ATPase, ATPase_P-typ_cation-transptr_N, P-type_ATPase_IIC

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
body of stomach	1
cardia of stomach	1
pylorus	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
ATP4A	137	tissue_specific	marker	cardia of stomach, pylorus, body of stomach

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
ATP4A	3,440

Structural data

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

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
ATP4A	P20648	88.70

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 3. 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
Ion transport by P-type ATPases	1	207.6×	0.014	ATP4A
Ion channel transport	1	96.0×	0.016	ATP4A
Transport of small molecules	1	25.1×	0.040	ATP4A

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
regulation of proton transport	1	5617.3×	0.002	ATP4A
pH reduction	1	2407.4×	0.002	ATP4A
sodium ion export across plasma membrane	1	1053.2×	0.003	ATP4A
intracellular potassium ion homeostasis	1	991.3×	0.003	ATP4A
intracellular sodium ion homeostasis	1	766.0×	0.003	ATP4A
potassium ion import across plasma membrane	1	366.4×	0.005	ATP4A
proton transmembrane transport	1	312.1×	0.005	ATP4A
monoatomic ion transmembrane transport	1	208.1×	0.006	ATP4A
potassium ion transmembrane transport	1	135.9×	0.008	ATP4A
response to xenobiotic stimulus	1	69.1×	0.014	ATP4A

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) 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.

Symbol	Example approved molecule
ATP4A	PANTOPRAZOLE

Top cohort targets by molecule count

Symbol	Molecules	Max phase
ATP4A	5	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
PANTOPRAZOLE	4	ATP4A
OMEPRAZOLE	4	ATP4A
RANITIDINE	4	ATP4A
CIMETIDINE	4	ATP4A
LANSOPRAZOLE	4	ATP4A

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
ATP4A	17	Binding:13, Functional:4

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
ATP4A	7.2.2.19	H+/K+-exchanging ATPase

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).

Drug repurposing candidates

5 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.

Compound	Max phase	Cohort target (bioactivity)
PANTOPRAZOLE	4	ATP4A
OMEPRAZOLE	4	ATP4A
RANITIDINE	4	ATP4A
CIMETIDINE	4	ATP4A
LANSOPRAZOLE	4	ATP4A

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	ATP4A
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	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.