Nasopharyngeal carcinoma, susceptibility to, 3

Summary

Nasopharyngeal carcinoma, susceptibility to, 3 (MONDO:0014902) is a cancer with 1 cohort gene.

At a glance

• Classification: Cancer
• Cohort genes: 1
• ClinVar variants: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	nasopharyngeal carcinoma, susceptibility to, 3
Mondo ID	MONDO:0014902
OMIM	617075
UMLS	C4310729
MedGen	934696
GARD	0027863
Is cancer (heuristic)	yes

Also known as: MST1R nasopharyngeal carcinoma · nasopharyngeal carcinoma caused by mutation in MST1R · nasopharyngeal carcinoma, susceptibility to, 3 · nasopharyngeal carcinoma, susceptibility to, 3; NPCA3 · nasopharyngeal carcinoma, susceptibility to, type 3 · NPCA3

Data availability: 3 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › hereditary neoplastic syndrome › nasopharyngeal carcinoma, susceptibility to, 3

Related subtypes (116): mosaic variegated aneuploidy syndrome, tuberous sclerosis, hereditary breast ovarian cancer syndrome, hereditary multiple osteochondromas, nevoid basal cell carcinoma syndrome, leukemia, chronic lymphocytic, susceptibility to, 2, blue rubber bleb nevus, cherubism, Beckwith-Wiedemann syndrome, multiple self-healing squamous epithelioma, erythroleukemia, familial, susceptibility to, goiter, multinodular 1, with or without Sertoli-Leydig cell tumors, hyperparathyroidism 2 with jaw tumors, Kaposi sarcoma, susceptibility to, hereditary leiomyomatosis and renal cell cancer, susceptibility to uveal melanoma, melanoma and neural system tumor syndrome, nasopharyngeal carcinoma, susceptibility to, 2, WAGR syndrome, neuroblastoma, susceptibility to, 1, Rothmund-Thomson syndrome, mismatch repair cancer syndrome 1, Wiskott-Aldrich syndrome, N syndrome, hereditary thrombocytopenia and hematologic cancer predisposition syndrome, prostate cancer/brain cancer susceptibility, Brooke-Spiegler syndrome, pancreatic cancer, susceptibility to, 1, Carney-Stratakis syndrome, nasopharyngeal carcinoma, susceptibility to, 1, ovarian cancer, susceptibility to, 1, colorectal cancer, susceptibility to, 1, lung cancer susceptibility 1, leukemia, chronic lymphocytic, susceptibility to, 1, Kostmann syndrome, colorectal cancer, susceptibility to, 2, colorectal cancer, susceptibility to, 3, colorectal cancer, susceptibility to, 5, colorectal cancer, susceptibility to, 6, colorectal cancer, susceptibility to, 7, leukemia, chronic lymphocytic, susceptibility to, 3, leukemia, chronic lymphocytic, susceptibility to, 4, leukemia, chronic lymphocytic, susceptibility to, 5, lung cancer susceptibility 3, colorectal cancer, susceptibility to, 8, colorectal cancer, susceptibility to, 9, colorectal cancer, susceptibility to, 10, colorectal cancer, susceptibility to, 11, lung cancer susceptibility 4, neuroblastoma, susceptibility to, 3, neuroblastoma, susceptibility to, 4, neuroblastoma, susceptibility to, 5, neuroblastoma, susceptibility to, 6, leukemia, acute lymphocytic, susceptibility to, 1, leukemia, acute lymphocytic, susceptibility to, 2, lung cancer susceptibility 5, BAP1-related tumor predisposition syndrome, familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome, Maffucci syndrome, basal cell carcinoma, susceptibility to, 7, colorectal cancer, susceptibility to, 12, leukemia, acute lymphoblastic, susceptibility to, 3, cholangiocarcinoma, susceptibility to, progeroid features-hepatocellular carcinoma predisposition syndrome, neuroblastoma, susceptibility to, 7, DDX41-related hematologic malignancy predisposition syndrome, familial isolated hyperparathyroidism, intestinal polyposis syndrome, dyskeratosis congenita, familial rhabdoid tumor, multiple endocrine neoplasia, hereditary pheochromocytoma-paraganglioma, PTEN hamartoma tumor syndrome, familial multiple fibrofolliculoma, hereditary retinoblastoma, familial atypical multiple mole melanoma syndrome, hereditary nonpolyposis colon cancer, Li-Fraumeni syndrome, Cobb syndrome, neurofibromatosis, susceptibility to familial cutaneous melanoma, pancreatic cancer, susceptibility to, 5, leukemia, acute myeloid, susceptibility to, diffuse gastric and lobular breast cancer syndrome with or without cleft lip and/or palate, glioma susceptibility, hemangioma, capillary infantile, susceptibility to, CDH1-related diffuse gastric and lobular breast cancer syndrome, NTHL1-deficiency tumor predisposition syndrome, SAMD9-related spectrum and myeloid neoplasm risk, neuroblastoma, susceptibility to, 2, BARD1-related cancer predisposition, BRCA1-related cancer predisposition, BRCA2-related cancer predisposition, ATM-related cancer predisposition, CHEK2-related cancer predisposition, PALB2-related cancer predisposition, RAD51C-related cancer predisposition, RAD51D-related cancer predisposition, Li-fraumeni-like syndrome, breast cancer, familial, susceptibility to, 1, breast cancer, familial, susceptibility to, 2, breast cancer, familial, susceptibility to, 3, colorectal cancer, susceptibility to, 4, colorectal cancer, susceptibility to, on chromosome 15, ovarian cancer, familial, susceptibility to, 1, ovarian cancer, familial, susceptibility to, 2, ovarian cancer, familial, susceptibility to, 3, inherited hematologic cancer-predisposing syndrome, mosaic neurofibromatosis/schwannomatosis, tumor predisposition syndrome 2, prostate cancer, hereditary, X-linked 3, follicular lymphoma, susceptibility to, GPR161-related medulloblastoma predisposition, SAMD9L-related spectrum and myeloid neoplasm risk, HAVCR2-related cancer predisposition, EGLN1-related erythrocytosis and pheochromocytoma/paraganglioma predisposition

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

3 retrieved; paginated sample, class counts are floors:

1 risk factor, 1 uncertain significance, 1 benign/likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
253185	NM_002447.4(MST1R):c.917G>A (p.Arg306His)	MST1R	risk factor	no assertion criteria provided
3779966	NM_002447.4(MST1R):c.1231-1G>C	MST1R	Uncertain significance	criteria provided, single submitter
727441	NM_002447.4(MST1R):c.1861A>T (p.Lys621Ter)	MST1R	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 1 · Orphanet: 0 · 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
MST1R	Limited	Autosomal dominant	nasopharyngeal carcinoma, susceptibility to, 3

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
MST1R	HGNC:7381	ENSG00000164078	Q04912	Macrophage-stimulating protein receptor	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
MST1R	Macrophage-stimulating protein receptor	Receptor tyrosine kinase that transduces signals from the extracellular matrix into the cytoplasm by binding to MST1 ligand.

Protein-family classification

Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0

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
Kinase	1	27.7×	0.036

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
MST1R	Kinase	yes	2.7.10.1	Prot_kinase_dom, Ser-Thr/Tyr_kinase_cat_dom, Semap_dom

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
lower esophagus mucosa	1
mucosa of transverse colon	1
skin of leg	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
MST1R	191	broad	marker	mucosa of transverse colon, skin of leg, lower esophagus mucosa

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
MST1R	3,083

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
MST1R	Q04912	4

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
Signaling by MST1	1	2284.0×	0.001	MST1R
Signaling by Receptor Tyrosine Kinases	1	51.7×	0.029	MST1R
Signal Transduction	1	10.2×	0.098	MST1R

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
positive regulation of MAP kinase activity	1	648.1×	0.014	MST1R
phagocytosis	1	240.7×	0.014	MST1R
defense response	1	216.1×	0.014	MST1R
single fertilization	1	183.2×	0.014	MST1R
cell surface receptor protein tyrosine kinase signaling pathway	1	173.7×	0.014	MST1R
response to virus	1	144.0×	0.014	MST1R
positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	1	78.4×	0.022	MST1R
cell migration	1	61.5×	0.024	MST1R
nervous system development	1	45.9×	0.029	MST1R
positive regulation of cell population proliferation	1	33.6×	0.032	MST1R
innate immune response	1	33.6×	0.032	MST1R
signal transduction	1	16.1×	0.062	MST1R

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
MST1R	AFATINIB

Top cohort targets by molecule count

Symbol	Molecules	Max phase
MST1R	42	4

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
AFATINIB	4	MST1R
NERATINIB	4	MST1R
INFIGRATINIB PHOSPHATE	4	MST1R
INFIGRATINIB	4	MST1R
PALBOCICLIB	4	MST1R
ENTRECTINIB	4	MST1R
FOSTAMATINIB	4	MST1R
CABOZANTINIB	4	MST1R
VANDETANIB	4	MST1R
BOSUTINIB	4	MST1R
GILTERITINIB	4	MST1R
CRIZOTINIB	4	MST1R
LINIFANIB	3	MST1R
BARASERTIB	3	MST1R
CEDIRANIB	3	MST1R
DOVITINIB	3	MST1R
LESTAURTINIB	3	MST1R
FORETINIB	2	MST1R
REBASTINIB	2	MST1R
MK-2461	2	MST1R
CENISERTIB	2	MST1R
ILORASERTIB	2	MST1R
DEFOSBARASERTIB	2	MST1R
OSI-632	2	MST1R
GOLVATINIB	2	MST1R
MERESTINIB	2	MST1R
GLESATINIB	2	MST1R
BMS-777607	2	MST1R
R-406	2	MST1R
MILCICLIB	2	MST1R

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 1.

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

Symbol	Assays	Type breakdown
MST1R	384	Binding:382, Functional:2

Cohort enzymes (BRENDA EC)

Symbol	EC numbers	Names
MST1R	2.7.10.1	receptor protein-tyrosine kinase

Cohort genes with high screening signal

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

Symbol	ChEMBL assays
MST1R	384

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

30 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)
AFATINIB	4	MST1R
NERATINIB	4	MST1R
INFIGRATINIB PHOSPHATE	4	MST1R
INFIGRATINIB	4	MST1R
PALBOCICLIB	4	MST1R
ENTRECTINIB	4	MST1R
FOSTAMATINIB	4	MST1R
CABOZANTINIB	4	MST1R
VANDETANIB	4	MST1R
BOSUTINIB	4	MST1R
GILTERITINIB	4	MST1R
CRIZOTINIB	4	MST1R
LINIFANIB	3	MST1R
BARASERTIB	3	MST1R
CEDIRANIB	3	MST1R
DOVITINIB	3	MST1R
LESTAURTINIB	3	MST1R
FORETINIB	2	MST1R
REBASTINIB	2	MST1R
MK-2461	2	MST1R
CENISERTIB	2	MST1R
ILORASERTIB	2	MST1R
DEFOSBARASERTIB	2	MST1R
OSI-632	2	MST1R
GOLVATINIB	2	MST1R
MERESTINIB	2	MST1R
GLESATINIB	2	MST1R
BMS-777607	2	MST1R
R-406	2	MST1R
MILCICLIB	2	MST1R

Druggability pyramid

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

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	1	MST1R
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.