Sialolithiasis

Summary

Sialolithiasis (MONDO:0006970) is a disease with 26 GWAS associations across 6 studies and 1 clinical trial. A subtype of salivary gland disorder — broader associated-gene and molecular evidence is on the parent page (see Disease family below).

At a glance

• GWAS associations: 26
• Clinical trials: 1

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	sialolithiasis
Mondo ID	MONDO:0006970
EFO	EFO:1001180
MeSH	D015494
DOID	DOID:12905
ICD-10-CM	K11.5
ICD-11	1984849248
SNOMED CT	28826002
UMLS	C0036091
MedGen	48536
MedDRA	10040631
Is cancer (heuristic)	no

Also known as: sialolith · Stone of salivary gland or duct

Data availability: 26 GWAS associations (6 studies).

Disease family

This is a subtype of salivary gland 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 › mouth disorder › salivary gland disorder › sialolithiasis

Related subtypes (8): submandibular gland disorder, benign lymphoepithelial lesion of salivary gland, mucocele of salivary gland, parotid disorder, necrotizing sialometaplasia, sialadenitis, Sjogren syndrome, tumor of salivary gland

Genetics & variants

GWAS landscape

26 GWAS associations across 6 studies. Top hits map to 14 distinct genes (as reported by GWAS).

Top associations by p-value

rsID	p-value	Gene	Risk allele	Odds ratio
rs542305908	3e-14	ABI1	T	4.19
rs183191767	1e-13	WARS2	C	3.42
rs149298885	2e-13	LINC01163 - LINC02667	G	3.4
rs140037248	2e-13	CRACR2A	A	4.87
rs180791941	5e-13	EPHB1	A	4.47
rs192386171	9e-13	RCOR1 - TRAF3	C	3.65
rs191277764	2e-12	COL13A1	G	2.59
rs189453683	2e-12	KANK3 - ANGPTL4	G	3.9
rs184629645	2e-12	ERG	G	2.4
rs532124815	3e-12	RNA5SP279 - SMARCA2	A	3.79
rs189659702	3e-12	EIF2AK3	A	2.75
rs142507881	3e-12	FECHP1 - KRT8P18	G	2.32
rs573299485	3e-12	HSPD1P15 - CDH18	T	4.08
rs146944865	4e-12	MED28P5 - LINC02553	G	3.19
rs551958855	4e-12	ATG4B	G	3
rs533424065	5e-12	PRKN	C	5.19
rs182413230	1e-11	ADD2	G	2.94
rs1891953	1e-11	POLR1D - GSX1	C	3.06
rs577517664	2e-11	LINC02325 - LINC02291	C	4.45
rs189361418	3e-11	CCNY	G	3.38
rs530371276	3e-11	LINC02500 - TENM3-AS1	C	3.55
rs571223503	4e-11	CPAMD8P1 - U3	C	3.19
rs554478585	4e-11	DPP6	T	4.95
rs533022433	4e-11	FLYWCH1	C	3.33
rs550873298	4e-11	PDLIM5 - BMPR1B-DT	C	4.1
rs117751932	5e-07	LINC01019	?

Top studies (by case count)

Study	Lead author	Year	Cases	Controls	Title
GCST90482127	Verma A	2024	449	450,273	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90436297	Zhou W	2018	314	403,323	Efficiently controlling for case-control imbalance and sample relatedness in large-scale genetic association studies.
GCST90044116	Jiang L	2021	291	456,057	A generalized linear mixed model association tool for biobank-scale data.
GCST90480287	Verma A	2024	248	121,451	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90482126	Verma A	2024	248	121,451	Diversity and scale: Genetic architecture of 2068 traits in the VA Million Veteran Program.
GCST90652161	Liu TY	2025	236	215,085	Diversity and longitudinal records: Genetic architecture of disease associations and polygenic risk in the Taiwanese Han population.

Variant details and genetic-evidence tiers

Tier distribution (top 50 variants)

Tier	Variants
Tier 1: coding	0
Tier 2: splice/UTR	1
Tier 3: regulatory	1
Tier 4: intronic/intergenic	24

MAF distribution

Bucket	Variants
common (>=0.05)	0
low_freq (0.01-0.05)	0
rare (<0.01)	25
unknown	1

Functional consequences

Consequence	Count
intron_variant	14
intergenic_variant	9
regulatory_region_variant	1
3_prime_UTR_variant	1
non_coding_transcript_exon_variant	1

Top variants

rsID	Chr	Pos	Alleles	MAF	Consequence	Gene	p-value	Tier
rs542305908	10	26774627	T>C	0	intron_variant	ABI1	3e-14	Tier 4: intronic/intergenic
rs183191767	1	119106780	C>T	0.001	intron_variant	WARS2	1e-13	Tier 4: intronic/intergenic
rs149298885	10	128834918	G>A	0	intergenic_variant	LINC01163 - LINC02667	2e-13	Tier 4: intronic/intergenic
rs140037248	12	3687467	A>G	0.001	intron_variant	CRACR2A	2e-13	Tier 4: intronic/intergenic
rs180791941	3	134890127	A>C,T	0	intron_variant	EPHB1	5e-13	Tier 4: intronic/intergenic
rs192386171	14	102748193	C>T	0	intergenic_variant	RCOR1 - TRAF3	9e-13	Tier 4: intronic/intergenic
rs191277764	10	69930580	G>A,T	0.001	intron_variant	COL13A1	2e-12	Tier 4: intronic/intergenic
rs189453683	19	8363166	G>C,T	0	regulatory_region_variant	KANK3 - ANGPTL4	2e-12	Tier 3: regulatory
rs184629645	21	38414067	G>A,T	0.001	intron_variant	ERG	2e-12	Tier 4: intronic/intergenic
rs532124815	9	1574859	A>C,G	0	intergenic_variant	RNA5SP279 - SMARCA2	3e-12	Tier 4: intronic/intergenic
rs189659702	2	88592222	A>G	0.002	intron_variant	EIF2AK3	3e-12	Tier 4: intronic/intergenic
rs142507881	3	35102860	G>A	0.001	intergenic_variant	FECHP1 - KRT8P18	3e-12	Tier 4: intronic/intergenic
rs573299485	5	19321992	T>C	0.001	intergenic_variant	HSPD1P15 - CDH18	3e-12	Tier 4: intronic/intergenic
rs146944865	11	97009238	G>T	0.001	intergenic_variant	MED28P5 - LINC02553	4e-12	Tier 4: intronic/intergenic
rs551958855	2	241657933	G>A	0	intron_variant	ATG4B	4e-12	Tier 4: intronic/intergenic
rs533424065	6	161967174	C>T	0	intron_variant	PRKN	5e-12	Tier 4: intronic/intergenic
rs182413230	2	70660460	G>A,T	0.001	3_prime_UTR_variant	ADD2	1e-11	Tier 2: splice/UTR
rs1891953	13	27774909	C>T	0.001	intergenic_variant	POLR1D - GSX1	1e-11	Tier 4: intronic/intergenic
rs577517664	14	97598451	C>T	0.001	intergenic_variant	LINC02325 - LINC02291	2e-11	Tier 4: intronic/intergenic
rs189361418	10	35350667	G>A	0.001	intron_variant	CCNY	3e-11	Tier 4: intronic/intergenic
rs530371276	4	181736246	C>T	0	intron_variant	LINC02500 - TENM3-AS1	3e-11	Tier 4: intronic/intergenic
rs571223503	7	10105845	C>G,T	0.001	intergenic_variant	CPAMD8P1 - U3	4e-11	Tier 4: intronic/intergenic
rs554478585	7	153832210	T>C,G	0	intron_variant	DPP6	4e-11	Tier 4: intronic/intergenic
rs533022433	16	2915778	C>A,G	0	intron_variant	FLYWCH1	4e-11	Tier 4: intronic/intergenic
rs550873298	4	94682149	C>T	0	intron_variant	PDLIM5 - BMPR1B-DT	4e-11	Tier 4: intronic/intergenic
rs117751932	5	3504171	C>T		non_coding_transcript_exon_variant	LINC01019	5e-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: 1.

Phase distribution (across all retrieved trials)

Phase	Trials
Not specified	1

Top trials by phase / activity

NCT	Phase	Status	Title
NCT04695444	Not specified	COMPLETED	Effect of Different Nasotracheal Tubes on Tube Passage