Tooth disorder

Summary

Tooth disorder (MONDO:0006999) is a disease (an umbrella term covering 11 Mondo subtypes) with 20 GWAS associations across 47 studies and 3 clinical trials. A subtype of skeletal system disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• Umbrella term: 11 Mondo subtypes
• GWAS associations: 20
• Clinical trials: 3

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	tooth disorder
Mondo ID	MONDO:0006999
EFO	EFO:1001216
MeSH	D014076
DOID	DOID:1091
NCIT	C35077
SNOMED CT	234947003
UMLS	C0040435
MedGen	11852
Anatomy (UBERON)	UBERON:0001091
Is cancer (heuristic)	no

Also known as: calcareous tooth disease · calcareous tooth disease or disorder · dental disorder · disease of calcareous tooth · disease or disorder of calcareous tooth · disorder of calcareous tooth · tooth disorder

Data availability: 20 GWAS associations (47 studies).

Disease family

This is a subtype of skeletal 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 › skeletal system disorder › tooth disorder

Related subtypes (47): symphalangism, cartilage cancer, vertebral column disorder, patellar tendinitis, necrosis of ear ossicle, laryngeal cartilage cancer, ochronosis disorder, chondroma, periodontal disorder, posterior cranial fossa meningioma, anterior cranial fossa meningioma, middle cranial fossa meningioma, bone marrow disorder, cranial nodular fasciitis, flatfoot, bone disorder, skeletal tuberculosis, arthropathy, primary basilar invagination, Brachymorphism-onychodysplasia-dysphalangism syndrome, cherubism, fibrodysplasia ossificans progressiva, Marfan syndrome, Buschke-Ollendorff syndrome, scalp defects-postaxial polydactyly syndrome, cartilage-hair hypoplasia, Teebi-Shaltout syndrome, short stature-auditory canal atresia-mandibular hypoplasia-skeletal anomalies syndrome, ossification of the posterior longitudinal ligament of the spine, temtamy preaxial brachydactyly syndrome, metaphyseal undermodeling, spondylar dysplasia, and overgrowth, Al-Gazali syndrome, brachydactyly-syndactyly syndrome, endocrine-cerebro-osteodysplasia syndrome, metaphyseal chondromatosis with D-2-hydroxyglutaric aciduria, multiple congenital anomalies-hypotonia-seizures syndrome 3, Rienhoff syndrome, Coffin-Siris syndrome, microcephaly-brachydactyly-kyphoscoliosis syndrome, cartilage development disorder, syndactyly, polydactyly, brachydactyly, sternal neoplasm, short stature, amelogenesis imperfecta, and skeletal dysplasia with scoliosis, skeletal ligament disorder, brachydactyly-syndactyly-oligodactyly syndrome

Subtypes (11): dental abscess, tooth hard tissue disease, tooth erosion, non-bacterial, dental pulp disorder, tooth agenesis, dental fluorosis, anodontia, taurodontism, dentinogenesis imperfecta, odontogenic neoplasm, dental radicular dysplasia

Genetics & variants

GWAS landscape

20 GWAS associations across 47 studies. Top hits map to 10 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs189050011	8e-14	SIRT1	A	2.19
rs549810223	1e-12	NIHCOLE - RNU6-334P	G	2.97
rs570547461	1e-12	RNA5SP189 - LINC01950	A	2.5
rs183906425	3e-12	CNNM1	C	2.33
rs577513954	4e-12	TLE1	G	2.5
rs566924319	9e-12	LINC01544 - RNF152	G	3.22
rs146013551	1e-11	PKHD1	T	2.36
rs543387342	1e-11	HECW1	G	2.16
rs560103440	1e-11	GRM5 - TYR	A	1.95
rs186736823	2e-11	LINC02501 - LINC02506	C	4.59
rs187431382	2e-11	ABCG2 - PPM1K	G	2.21
rs573908889	3e-11	LINC02498 - MIR572	A	3.19
rs572247349	3e-11	RNU5B-6P - RNU6-839P	G	3.54
rs575390316	3e-11	SMOX	C	3.28
rs545900533	3e-11	RRBP1	G	2.58
rs182024483	4e-11	LINC01951	G	3.99
rs183869688	4e-11	PCAT1	G	3.33
rs3815861	2e-07	PDGFC	?
rs160142	4e-07	GPC5 - LINC00363	?
rs7848039	2e-06	SPATA31D3 - SPATA31D2P	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90478276	Verma A	2024	82,431	338,710	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478252	Verma A	2024	65,820	359,654	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478275	Verma A	2024	38,143	71,476	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480842	Verma A	2024	38,143	71,476	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90478251	Verma A	2024	31,213	79,100	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90480847	Verma A	2024	31,213	79,100	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90079439	Backman JD	2021	18,873	156,336	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90083425	Backman JD	2021	18,873	156,336	Exome sequencing and analysis of 454,787 UK Biobank participants.
GCST90044344	Jiang L	2021	18,545	436,020	A generalized linear mixed model association tool for biobank-scale data.
GCST90478273	Verma A	2024	13,657	41,301	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	20

MAF distribution

Bucket	Variants
common (>=0.05)	3
low_freq (0.01-0.05)	0
rare (<0.01)	17
unknown	0

Functional consequences

Consequence	Count
intron_variant	10
intergenic_variant	8
synonymous_variant	2

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs189050011	10	67893562	A>G,T	0.001	intron_variant	SIRT1	8e-14	Tier 4: intronic/intergenic
rs549810223	5	104713919	G>C	0.001	intron_variant	NIHCOLE - RNU6-334P	1e-12	Tier 4: intronic/intergenic
rs570547461	5	106390379	A>C,G	0.001	intergenic_variant	RNA5SP189 - LINC01950	1e-12	Tier 4: intronic/intergenic
rs183906425	10	99330026	C>T	0.001	synonymous_variant	CNNM1	3e-12	Tier 4: intronic/intergenic
rs577513954	9	81587150	G>A,T	0.001	intron_variant	TLE1	4e-12	Tier 4: intronic/intergenic
rs566924319	18	61783120	G>A,T	0.001	intergenic_variant	LINC01544 - RNF152	9e-12	Tier 4: intronic/intergenic
rs146013551	6	51770816	T>C	0.002	intron_variant	PKHD1	1e-11	Tier 4: intronic/intergenic
rs543387342	7	43350053	G>T	0.001	intron_variant	HECW1	1e-11	Tier 4: intronic/intergenic
rs560103440	11	89156833	A>C,G,T	0.001	intergenic_variant	GRM5 - TYR	1e-11	Tier 4: intronic/intergenic
rs186736823	4	31659398	C>T	0	intergenic_variant	LINC02501 - LINC02506	2e-11	Tier 4: intronic/intergenic
rs187431382	4	88235420	G>A	0.002	intergenic_variant	ABCG2 - PPM1K	2e-11	Tier 4: intronic/intergenic
rs573908889	4	10986743	A>G	0	intergenic_variant	LINC02498 - MIR572	3e-11	Tier 4: intronic/intergenic
rs572247349	10	109235746	G>C	0	intergenic_variant	RNU5B-6P - RNU6-839P	3e-11	Tier 4: intronic/intergenic
rs575390316	20	4155086	C>T	0	intron_variant	SMOX	3e-11	Tier 4: intronic/intergenic
rs545900533	20	17649619	G>C	0.001	intron_variant	RRBP1	3e-11	Tier 4: intronic/intergenic
rs182024483	5	174938858	G>A,C	0	intron_variant	LINC01951	4e-11	Tier 4: intronic/intergenic
rs183869688	8	126745521	G>A,T	0	intron_variant	PCAT1	4e-11	Tier 4: intronic/intergenic
rs3815861	4	156763096	T>A,C	0.05	synonymous_variant	PDGFC	2e-07	Tier 4: intronic/intergenic
rs160142	13	92993790	T>C,G	0.05	intergenic_variant	GPC5 - LINC00363	4e-07	Tier 4: intronic/intergenic
rs7848039	9	81964103	T>A,G	0.05	intron_variant	SPATA31D3 - SPATA31D2P	2e-06	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

Drugs indicated for this disease

0 approved, 5 in late-stage (phase 3) trials. Disease-direct ChEMBL indications, not inferred from the associated-gene cohort below.

Drug	Development status
Hydrogen Peroxide	Phase 3 (in late-stage trials)
Melatonin	Phase 3 (in late-stage trials)
Silver	Phase 3 (in late-stage trials)
Sodium Fluoride	Phase 3 (in late-stage trials)
Stannous Fluoride	Phase 3 (in late-stage trials)

Earlier-phase candidates (phase 2, investigational — efficacy not yet established): Ginger, Ibuprofen, Ozone.

Clinical trials & evidence

Clinical trials

Clinical trials: 3.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	3

Top trials by phase / activity

NCT	Phase	Status	Title
NCT03967002	Not specified	ACTIVE_NOT_RECRUITING	Treatment of the Mandibular Dental Crowding With and Without Corticotomy Surgery
NCT07110220	Not specified	ENROLLING_BY_INVITATION	All-ceramic Restorations: a Retrospective and Prospective Study
NCT07170956	Not specified	NOT_YET_RECRUITING	Analysis of Tooth Root Number