Synovium disorder

Summary

Synovium disorder (MONDO:0056799) is a disease with 5 GWAS associations across 16 studies. A subtype of musculoskeletal system disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 5

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	synovium disorder
Mondo ID	MONDO:0056799
SNOMED CT	3519007
UMLS	C0263945
MedGen	538212
Anatomy (UBERON)	UBERON:0007616
Is cancer (heuristic)	no

Also known as: disease of layer of synovial tissue · disease or disorder of layer of synovial tissue · disorder of layer of synovial tissue · disorder of synovium · layer of synovial tissue disease · layer of synovial tissue disease or disorder

Data availability: 5 GWAS associations (16 studies).

Disease family

This is a subtype of musculoskeletal system disorder. 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 body system or component › musculoskeletal system disorder › synovium disorder

Related subtypes (21): autoimmune disorder of musculoskeletal system, musculoskeletal system benign neoplasm, musculoskeletal system cancer, Klippel-Feil syndrome, enthesopathy, muscle tissue disorder, fasciitis, skeletal system disorder, synovial chondromatosis, auriculoosteodysplasia, hypertrophic osteoarthropathy, primary, autosomal dominant, Upington disease, Ramon syndrome, osteoporosis-oculocutaneous hypopigmentation syndrome, short stature, Brussels type, wormian bone-multiple fractures-dentinogenesis imperfecta-skeletal dysplasia, CINCA syndrome, chondrodysplasia with joint dislocations, gPAPP type, ligament disorder, disease of the tendon, Short stature, Dauber-Argente type

Subtypes (4): synovial plica syndrome, synovitis, synovium neoplasm, synovial bursa disorder

Genetics & variants

GWAS landscape

5 GWAS associations across 16 studies. Top hits map to 4 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs145064964	2e-13	HDAC2-AS2	C	4.91
rs187398351	1e-12	CACNA2D3	A	3.91
rs374124853	5e-12	LINC01419 - TPM3P3	A	2.61
rs569032076	9e-12	LINC02159 - GABRB2	T	2.67
rs182131760	3e-11	GABRB3, GABRA5	C	3.19

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90478938	Verma A	2024	4,290	438,684	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478955	Verma A	2024	1,958	444,943	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90727095	Kim HI	2026	1,655	42,371	Exome sequencing and analysis of 44,028 British South Asians enriched for high autozygosity.
GCST90478937	Verma A	2024	1,033	118,804	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90481007	Verma A	2024	1,033	118,804	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478936	Verma A	2024	858	57,660	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90080523	Backman JD	2021	697	387,233	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90084509	Backman JD	2021	697	387,233	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90478954	Verma A	2024	686	119,677	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480519	Verma A	2024	686	119,677	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.

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	5

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	5
unknown	0

Functional consequences

Consequence	Count
intron_variant	4
intergenic_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs145064964	6	114041618	C>G,T	0	intron_variant	HDAC2-AS2	2e-13	Tier 4: intronic/intergenic
rs187398351	3	54742869	A>G	0	intron_variant	CACNA2D3	1e-12	Tier 4: intronic/intergenic
rs374124853	8	83962529	A>G	0.001	intron_variant	LINC01419 - TPM3P3	5e-12	Tier 4: intronic/intergenic
rs569032076	5	161228640	T>C,G	0	intergenic_variant	LINC02159 - GABRB2	9e-12	Tier 4: intronic/intergenic
rs182131760	15	26912320	C>T	0.001	intron_variant	GABRB3, GABRA5	3e-11	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.