Hereditary diffuse gastric adenocarcinoma

disease
On this page

Also known as diffuse gastric cancerfamilial diffuse cancer of stomachfamilial diffuse gastric cancerFDGCHDGChereditary diffuse cancer of stomachhereditary diffuse gastric cancersignet cell adenocarcinomasignet ring cell gastric carcinomasignet ring gastric carcinoma

Summary

Hereditary diffuse gastric adenocarcinoma (MONDO:0007648) is a disease caused by CDH1 (GenCC Definitive), with 6 cohort genes and 5 clinical trials.

At a glance

  • Prevalence: Unknown (Worldwide)
  • Causal gene: CDH1 (GenCC Definitive)
  • Cohort genes: 6
  • ClinVar variants: 4,701
  • Clinical trials: 5

Clinical features

Epidemiology

Prevalence records

1 prevalence record(s), Orphanet:

TypeClassValueGeographyValidation
Annual incidence1-9 / 100 0001.5EuropeNot yet validated

Identifiers

Disease identifiers

FieldValue
Canonical namehereditary diffuse gastric adenocarcinoma
Mondo IDMONDO:0007648
Orphanet26106
DOIDDOID:0080764
NCITC43295
SNOMED CT716859000
UMLSC1708349
MedGen310839
GARD0010900
Is cancer (heuristic)no

Also known as: diffuse gastric cancer · familial diffuse cancer of stomach · familial diffuse gastric cancer · FDGC · HDGC · hereditary diffuse cancer of stomach · hereditary diffuse gastric adenocarcinoma · hereditary diffuse gastric cancer · signet cell adenocarcinoma · signet ring cell gastric carcinoma · signet ring gastric carcinoma

Data availability: 4,701 ClinVar variants · 2 ClinGen variant curations · 4 GenCC gene-disease records · 1 cell line.

Disease family

Classification path: disease › human disease › disease by body system or component › digestive system disorderdigestive system cancergastric cancergastric carcinomagastric adenocarcinomadiffuse gastric adenocarcinomahereditary diffuse gastric adenocarcinoma

Related subtypes (1): gastric linitis plastica

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

600 retrieved; paginated sample, class counts are floors:

184 uncertain significance, 155 benign/likely benign, 122 likely benign, 54 conflicting classifications of pathogenicity, 46 pathogenic, 30 benign, 5 pathogenic/likely pathogenic, 4 likely pathogenic

ClinVarVariant (HGVS)GeneClassificationReview
1066643NM_004360.5(CDH1):c.1008+1G>TCDH1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1068969NM_004360.5(CDH1):c.1569T>G (p.Tyr523Ter)CDH1Pathogeniccriteria provided, multiple submitters, no conflicts
1069664NC_000016.10:g.68829654delCDH1Pathogeniccriteria provided, single submitter
1069750NM_004360.5(CDH1):c.1641del (p.Glu547fs)CDH1Pathogeniccriteria provided, single submitter
1069973NM_004360.5(CDH1):c.1920dup (p.Gln641fs)CDH1Pathogeniccriteria provided, single submitter
1070687NM_004360.5(CDH1):c.1616del (p.Thr539fs)CDH1Pathogeniccriteria provided, single submitter
1071176NC_000016.9:g.(?68835563)(68863710_?)delCDH1Pathogeniccriteria provided, single submitter
1071177NC_000016.9:g.(?68820946)(68842761_?)delCDH1Pathogeniccriteria provided, single submitter
1071833NM_004360.5(CDH1):c.150_151dup (p.Val51fs)CDH1Pathogeniccriteria provided, single submitter
1072002NM_004360.5(CDH1):c.1711+1dupCDH1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1072150NM_004360.5(CDH1):c.555del (p.Gly186fs)CDH1Pathogeniccriteria provided, multiple submitters, no conflicts
1072773NM_004360.5(CDH1):c.1356_1362del (p.His453fs)CDH1Pathogeniccriteria provided, single submitter
1072979NC_000016.9:g.(?68771319)(68835806_?)delCDH1Pathogeniccriteria provided, single submitter
1072980NC_000016.9:g.(?_68857535)_68864666delCDH1Pathogeniccriteria provided, single submitter
1072981NC_000016.9:g.(?68863547)(68867402_?)delCDH1Pathogeniccriteria provided, single submitter
1072982NC_000016.9:g.(?68772190)(68849672_?)delCDH1Pathogeniccriteria provided, single submitter
1074240NM_004360.5(CDH1):c.1695_1696insTT (p.Ile566fs)CDH1Pathogeniccriteria provided, single submitter
1074394NM_004360.5(CDH1):c.1878_1885del (p.Phe626fs)CDH1Pathogeniccriteria provided, multiple submitters, no conflicts
1075278NC_000016.10:g.68815516delCDH1Pathogeniccriteria provided, multiple submitters, no conflicts
1076986NC_000016.9:g.(?68867183)(68867402_?)delCDH1Pathogeniccriteria provided, single submitter
1196343NM_004360.5(CDH1):c.1577G>A (p.Trp526Ter)CDH1Pathogeniccriteria provided, multiple submitters, no conflicts
12234NM_004360.5(CDH1):c.781G>T (p.Glu261Ter)CDH1Pathogenicreviewed by expert panel
12237NM_004360.5(CDH1):c.2095C>T (p.Gln699Ter)CDH1Pathogenicreviewed by expert panel
12239NM_004360.5(CDH1):c.59G>A (p.Trp20Ter)CDH1Pathogenicreviewed by expert panel
12240NM_004360.5(CDH1):c.70G>T (p.Glu24Ter)CDH1Pathogenicreviewed by expert panel
12241NM_004360.5(CDH1):c.1792C>T (p.Arg598Ter)CDH1Pathogenicreviewed by expert panel
12244NM_004360.5(CDH1):c.1901C>T (p.Ala634Val)CDH1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
12251NC_000016.10:g.68602418_68796011delCDH1Pathogenicno assertion criteria provided
12252NM_004360.5(CDH1):c.2440-396_*224delinsGGACDH1Pathogenicno assertion criteria provided
127915NM_004360.5(CDH1):c.1565+1G>ACDH1Pathogenicreviewed by expert panel

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 18 · Orphanet: 20 · 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
CDH1DefinitiveAutosomal dominanthereditary diffuse gastric adenocarcinoma15
MAP3K6SupportiveAutosomal dominanthereditary diffuse gastric adenocarcinoma2
IL1BNo Known Disease RelationshipUnknownhereditary diffuse gastric adenocarcinoma

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
CDH1Orphanet:1331Familial prostate cancer
CDH1Orphanet:199306Cleft lip/palate
CDH1Orphanet:1997Blepharo-cheilo-odontic syndrome
CDH1Orphanet:227535Hereditary breast cancer
CDH1Orphanet:26106Hereditary diffuse gastric cancer
MAP3K6Orphanet:26106Hereditary diffuse gastric cancer
CTNNA1Orphanet:26106Hereditary diffuse gastric cancer
CTNNA1Orphanet:99001Butterfly-shaped pigment dystrophy
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
RAD54LOrphanet:227535Hereditary breast cancer

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
CDH1HGNC:1748ENSG00000039068P12830Cadherin-1gencc,clinvar
IL1BHGNC:5992ENSG00000125538P01584Interleukin-1 betagencc
MAP3K6HGNC:6858ENSG00000142733O95382Mitogen-activated protein kinase kinase kinase 6gencc
CTNNA1HGNC:2509ENSG00000044115P35221Catenin alpha-1clinvar
KRASHGNC:6407ENSG00000133703P01116GTPase KRasclinvar
RAD54LHGNC:9826ENSG00000085999Q92698DNA repair and recombination protein RAD54-likeclinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
CDH1Cadherin-1Cadherins are calcium-dependent cell adhesion proteins.
IL1BInterleukin-1 betaPotent pro-inflammatory cytokine.
MAP3K6Mitogen-activated protein kinase kinase kinase 6Component of a protein kinase signal transduction cascade.
CTNNA1Catenin alpha-1Associates with the cytoplasmic domain of a variety of cadherins.
KRASGTPase KRasRas proteins bind GDP/GTP and possess intrinsic GTPase activity.
RAD54LDNA repair and recombination protein RAD54-likeMultifunctional ATPase that plays a role in homologous recombination (HR) which is a major pathway for repairing DNA double-strand breaks (DSBs), single-stranded DNA (ssDNA) gaps, and stalled or collapsed replication forks.

Protein-family classification

Druggable: 3 · Difficult: 0 · Unknown: 3 · Druggable fraction: 0.5

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
Enzyme (other)24.0×0.249
Kinase14.6×0.297
Other/Unknown30.9×0.758

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
CDH1Other/UnknownnoCadherin_Y-type_LIR, Cadherin-like_dom, Cadherin_pro_dom
IL1BOther/UnknownnoIL-1_fam, IL-1_propep, IL1/FGF
MAP3K6Kinaseyes2.7.11.25Prot_kinase_dom, Ser/Thr_kinase_AS, Kinase-like_dom_sf
CTNNA1Other/UnknownnoVinculin_CS, Alpha_catenin, Vinculin/catenin
KRASEnzyme (other)yes3.6.5.2Small_GTPase, Small_GTP-bd, Small_GTPase_Ras-type
RAD54LEnzyme (other)yes3.6.4.B9SNF2_N, Helicase_C-like, Helicase_ATP-bd

Expression context

Cohort genes with no expression data: 0.

5 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)6
unknown0

Top tissues across cohort

TissueCohort genes
esophagus squamous epithelium1
gingival epithelium1
jejunal mucosa1
granulocyte1
monocyte1
periodontal ligament1
lower esophagus mucosa1
right lung1
skin of abdomen1
amniotic fluid1
calcaneal tendon1
colonic epithelium1
nipple1
pylorus1
trigeminal ganglion1
left testis1
right testis1
ventricular zone1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
CDH1245broadmarkerjejunal mucosa, esophagus squamous epithelium, gingival epithelium
IL1B228ubiquitousmarkerperiodontal ligament, granulocyte, monocyte
MAP3K6227ubiquitousmarkerlower esophagus mucosa, right lung, skin of abdomen
CTNNA1305ubiquitousmarkercolonic epithelium, calcaneal tendon, amniotic fluid
KRAS298ubiquitousmarkertrigeminal ganglion, pylorus, nipple
RAD54L173ubiquitousyesleft testis, right testis, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 2.

Hub genes (top 10 by interactor count)

SymbolInteractor count
KRAS14,509
CDH18,738
IL1B8,564
CTNNA13,128
RAD54L2,927
MAP3K6941

Intra-cohort edges

ABSources
CDH1CTNNA1intact, string_interaction
CTNNA1MAP3K6string_interaction

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
KRASP01116511
IL1BP0158464
CDH1P1283022
CTNNA1P3522110
RAD54LQ926981

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
MAP3K6O9538275.36

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 129. Enrichment computed across 6 evidence-associated genes (4 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 4 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Regulation of CDH1 Function2475.8×8e-04CDH1, CTNNA1
SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST)2248.3×0.001CDH1, CTNNA1
RHO GTPases activate IQGAPs2173.0×0.002CDH1, CTNNA1
Adherens junctions interactions2124.1×0.003CDH1, CTNNA1
Degradation of CDH1298.5×0.004CDH1, CTNNA1
Activation of STAT3 by cadherin engagement281.6×0.005CDH1, CTNNA1
Signaling by RAS GAP mutants1951.7×0.015KRAS
Signaling by RAS GTPase mutants1951.7×0.015KRAS
Activation of RAS in B cells1571.0×0.015KRAS
CASP4-mediated substrate cleavage1571.0×0.015IL1B
CASP5-mediated substrate cleavage1571.0×0.015IL1B
CLEC7A/inflammasome pathway1475.8×0.015IL1B
RAS signaling downstream of NF1 loss-of-function variants1407.9×0.015KRAS
Estrogen-stimulated signaling through PRKCZ1407.9×0.015KRAS
CDH11 homotypic and heterotypic interactions1407.9×0.015CTNNA1
SOS-mediated signalling1356.9×0.015KRAS
Epithelial-Mesenchymal Transition (EMT) during gastrulation1356.9×0.015CDH1
Regulation of CDH19 Expression and Function1356.9×0.015CTNNA1
Interleukin-1 processing1317.2×0.015IL1B
InlA-mediated entry of Listeria monocytogenes into host cells1317.2×0.015CDH1
Activated NTRK3 signals through RAS1317.2×0.015KRAS
EGFR Transactivation by Gastrin1285.5×0.015KRAS
SHC-related events triggered by IGF1R1285.5×0.015KRAS
RUNX3 regulates p14-ARF1285.5×0.015KRAS
Activated NTRK2 signals through RAS1285.5×0.015KRAS
Apoptotic cleavage of cell adhesion proteins1259.6×0.015CDH1
MET activates RAS signaling1259.6×0.015KRAS
Listeria monocytogenes entry into host cells1259.6×0.015CDH1
Regulation of CDH11 function1259.6×0.015CTNNA1
Regulation of CDH1 mRNA translation by microRNAs1259.6×0.015CDH1

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
cellular response to indole-3-methanol21123.5×2e-04CDH1, CTNNA1
positive regulation of glial cell proliferation2234.1×0.003IL1B, KRAS
extrinsic apoptotic signaling pathway in absence of ligand2156.0×0.004CTNNA1, IL1B
negative regulation of extrinsic apoptotic signaling pathway in absence of ligand2137.0×0.004CTNNA1, IL1B
JNK cascade290.6×0.007IL1B, MAP3K6
response to mineralocorticoid12808.7×0.009KRAS
positive regulation of cell adhesion molecule production12808.7×0.009IL1B
positive regulation of T cell mediated immunity11404.3×0.010IL1B
positive regulation of complement activation11404.3×0.010IL1B
regulation of nitric-oxide synthase activity11404.3×0.010IL1B
positive regulation of RNA biosynthetic process11404.3×0.010IL1B
negative regulation of gap junction assembly11404.3×0.010IL1B
fever generation1936.2×0.010IL1B
forebrain astrocyte development1936.2×0.010KRAS
monocyte aggregation1936.2×0.010IL1B
response to heparin1936.2×0.010CDH1
smooth muscle adaptation1702.2×0.010IL1B
positive regulation of fever generation1702.2×0.010IL1B
response to isolation stress1702.2×0.010KRAS
double-strand break repair via synthesis-dependent strand annealing1702.2×0.010RAD54L
negative regulation of adiponectin secretion1702.2×0.010IL1B
regulation of protein catabolic process at postsynapse, modulating synaptic transmission1702.2×0.010CDH1
negative regulation of integrin-mediated signaling pathway1702.2×0.010CTNNA1
cytokine-mediated signaling pathway243.5×0.010IL1B, KRAS
cell-cell adhesion233.8×0.010CDH1, CTNNA1
positive regulation of platelet-derived growth factor receptor signaling pathway1561.7×0.010IL1B
negative regulation of D-glucose transmembrane transport1561.7×0.010IL1B
hyaluronan biosynthetic process1561.7×0.010IL1B
negative regulation of lipid metabolic process1561.7×0.010IL1B
positive regulation of tight junction disassembly1561.7×0.010IL1B

Therapeutics

Drug target analysis

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

Druggability breadth: 6 of 6 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.

SymbolExample approved molecule
IL1BPOMALIDOMIDE
MAP3K6LENVATINIB
KRASVEMURAFENIB

Top cohort targets by molecule count

SymbolMoleculesMax phase
KRAS114
MAP3K664
IL1B44
RAD54L12
CDH100
CTNNA100

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
POMALIDOMIDE4IL1B
LENALIDOMIDE4IL1B
LENVATINIB4MAP3K6
VEMURAFENIB4KRAS
DABRAFENIB4KRAS
LONAFARNIB4KRAS
SOTORASIB4KRAS
ADAGRASIB4KRAS
IBERDOMIDE3IL1B
SELONSERTIB3MAP3K6
LESTAURTINIB3MAP3K6
OPNURASIB3KRAS
AVADOMIDE2IL1B
UCN-012MAP3K6
DIVARASIB2KRAS
GLECIRASIB2KRAS
STREPTONIGRIN2RAD54L
PF-038147351MAP3K6
AST-4871MAP3K6
BMS-2146621KRAS
LY-30091201KRAS
MRTX-11331KRAS

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

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

SymbolAssaysType breakdown
KRAS861Binding:829, Functional:32
MAP3K6103Binding:103
IL1B26Binding:26
CDH118Binding:18
RAD54L3Functional:2, Binding:1
CTNNA12Binding:2

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
MAP3K62.7.11.25mitogen-activated protein kinase kinase kinase
KRAS3.6.5.2small monomeric GTPase
RAD54L3.6.4.B9

Cohort genes with high screening signal

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

SymbolChEMBL assays
MAP3K6103
KRAS861

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

22 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)
POMALIDOMIDE4IL1B
LENALIDOMIDE4IL1B
LENVATINIB4MAP3K6
VEMURAFENIB4KRAS
DABRAFENIB4KRAS
LONAFARNIB4KRAS
SOTORASIB4KRAS
ADAGRASIB4KRAS
IBERDOMIDE3IL1B
SELONSERTIB3MAP3K6
LESTAURTINIB3MAP3K6
OPNURASIB3KRAS
AVADOMIDE2IL1B
UCN-012MAP3K6
DIVARASIB2KRAS
GLECIRASIB2KRAS
STREPTONIGRIN2RAD54L
PF-038147351MAP3K6
AST-4871MAP3K6
BMS-2146621KRAS
LY-30091201KRAS
MRTX-11331KRAS

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3IL1B, MAP3K6, KRAS
BPhased (≥1) drug, not yet approved1RAD54L
CDruggable family + PDB, no drug0
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2CDH1, CTNNA1

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
CDH118
CTNNA12

Clinical trials & evidence

Clinical trials

Clinical trials: 5.

Phase distribution (across all retrieved trials)

PhaseTrials
Not specified5

Top trials by phase / activity

NCTPhaseStatusTitle
NCT00633607Not specifiedCOMPLETEDHereditary Colorectal and Associated Tumor Registry Study
NCT03030404Not specifiedCOMPLETEDHereditary Gastric Cancer Syndromes: An Integrated Genomic and Clinicopathologic Study of the Predisposition to Gastric Cancer
NCT03950908Not specifiedCOMPLETEDBiopsy Technique for Endoscopic Surveillance of Hereditary Diffuse Gastric Cancer
NCT04253106Not specifiedCOMPLETEDLiquid Biopsies for the Personalized Management of Patients with Hereditary Diffuse Gastric Cancer
NCT06163365Not specifiedUNKNOWNInherited Cancer Early Diagnosis (ICED) Study