Benign endocrine neoplasm

Summary

Benign endocrine neoplasm (MONDO:0000627) is a cancer (an umbrella term covering 14 Mondo subtypes) with 3 GWAS associations across 9 studies. A subtype of endocrine gland neoplasm — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Classification: Cancer
• Umbrella term: 14 Mondo subtypes
• GWAS associations: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	benign endocrine neoplasm
Mondo ID	MONDO:0000627
DOID	DOID:0060089
NCIT	C4621
SNOMED CT	92085000
UMLS	C0347524
MedGen	87577
Anatomy (UBERON)	UBERON:0002368
Is cancer (heuristic)	yes

Also known as: benign endocrine gland neoplasm · benign endocrine gland tumor · benign endocrine gland tumour · benign endocrine neoplasm · benign endocrine tumor · benign endocrine tumour · benign neoplasm of endocrine gland · benign neoplasm of the endocrine gland · benign tumor of endocrine gland · benign tumor of the endocrine gland · benign tumour of endocrine gland · benign tumour of the endocrine gland · endocrine gland benign neoplasm

Data availability: 3 GWAS associations (9 studies).

Disease family

This is a subtype of endocrine gland neoplasm. Genetic, therapeutic, and trial evidence is largely curated at the broader-term level — see the parent page for the associated-gene cohort and molecular evidence.

Classification path: disease › human disease › disease by etiologic mechanism › cancer or benign tumor › neoplastic disease or syndrome › neoplasm › endocrine gland neoplasm › benign endocrine neoplasm

Related subtypes (13): thymus neoplasm, granulosa cell tumor, thyroid tumor, pituitary tumor, familial tumoral calcinosis, neuroendocrine neoplasm, malignant endocrine neoplasm, non-functioning endocrine neoplasm, functioning endocrine neoplasm, adrenal gland neoplasm, pineal body neoplasm, tumor of parathyroid gland, liver and intrahepatic bile duct neoplasm

Subtypes (14): liver lipoma, liver hemangioma, bile duct papillary neoplasm, liver leiomyoma, benign carotid body paraganglioma, benign thyroid gland neoplasm, pineocytoma, hepatocellular adenoma, benign neoplasm of pituitary gland, benign neoplasm of parathyroid gland, benign neoplasm of adrenal gland, benign neoplasm of thymus, TMEM127-related tumor predisposition, MAX-related tumor predisposition

Genetics & variants

GWAS landscape

3 GWAS associations across 9 studies. Top hits map to 3 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs4442334	3e-14	AXDND1	A	0.14
chr1:179267474	4e-12		C	0.15
rs36235	1e-07	PRICKLE2, PRICKLE2-AS2	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90475630	Verma A	2024	5,212	442,850	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90477289	Verma A	2024	2,227	118,612	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90479856	Verma A	2024	2,227	118,612	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079693	Backman JD	2021	1,177	386,605	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083679	Backman JD	2021	1,177	386,605	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90435678	Zhou W	2018	876	407,399	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90651889	Liu TY	2025	815	234,488	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.
GCST90477288	Verma A	2024	680	58,906	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90726697	Kim HI	2026	141	43,885	Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	0
Tier 3: regulatory	0
Tier 4: intronic/intergenic	3

MAF distribution

Bucket	Variants
common (>=0.05)	3
low_freq (0.01-0.05)	0
rare (<0.01)	0
unknown	0

Functional consequences

Consequence	Count
intron_variant	2
unknown	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs4442334	1	179377693	A>G,T	0.24	intron_variant	AXDND1	3e-14	Tier 4: intronic/intergenic
chr1:179267474				0.25			4e-12	Tier 4: intronic/intergenic
rs36235	3	64104244	A>C,G,T	0.05	intron_variant	PRICKLE2, PRICKLE2-AS2	1e-07	Tier 4: intronic/intergenic

Genes & proteins

No associated-gene cohort resolved for this disease. Atlas builds the molecular and therapeutic sections — associated genes, protein families, druggability, pathways, interactions, and drug associations — by aggregating over a disease’s associated genes (resolved via GWAS / GenCC / ClinVar / CIViC), and none resolved here. This is expected for antibody-mediated, autoimmune, or otherwise non-gene-defined conditions; the curated evidence for this disease is its clinical features, GWAS susceptibility, and clinical trials (above).

Function

No pathway enrichment — requires an associated-gene cohort.

Therapeutics

No druggable-target or therapeutic data for this disease’s cohort.

Clinical trials & evidence

Clinical trials

Clinical trials: 0.