LRRC3C
Chr 17leucine rich repeat containing 3C
Predicted to be located in membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Jul 2025]
Clinical Summary— LRRC3C
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Population Constraint (gnomAD)
Low constraint (pLI 0.03) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
8 Pathogenic / Likely Pathogenic· 52 VUS of 62 total submissions
Some data sources returned errors (1)
ensembl: TimeoutError: The operation was aborted due to timeout
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
1.31LOEUF
pLI 0.029
Z-score 1.10
OE 0.51 (0.23–1.31)
Highly tolerant — LoF variants common in population
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.57Z-score
OE missense 0.87 (0.75–1.01)
131 obs / 150.6 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.51 (0.23–1.31)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.87 (0.75–1.01)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.95
0≤1.21.6
LoF obs/exp: 3 / 5.9Missense obs/exp: 131 / 150.6Syn Z: 0.33
ClinVar Variant Classifications
62 submitted variants in ClinVar
Classification Summary
Pathogenic8
VUS52
Likely Benign2
8
Pathogenic
52
VUS
2
Likely Benign
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 8 | 0 | 8 |
Likely Pathogenic | 0 | 0 | 0 | 0 | 0 |
VUS | 0 | 50 | 2 | 0 | 52 |
Likely Benign | 0 | 1 | 0 | 1 | 2 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 51 | 10 | 1 | 62 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
LRRC3C · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
OMIM — Genotype-Phenotype
No OMIM entries found.
External Resources
Links to major genomics databases and tools
Clinical Literature
Landmark / reviewRecent case evidence
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Gene Expression-Genotype Analysis Implicates GSDMA, GSDMB, and LRRC3C as Contributors to Inflammatory Bowel Disease Susceptibility.
Söderman J et al.·Biomed Res Int
2015Open Access
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Epigenome-wide association studies of meat traits in Chinese Yorkshire pigs highlights several DNA methylation loci and genes
Wang K et al.·Front Genet
2023
Association of Gasdermin B Gene GSDMB Polymorphisms with Risk of Allergic Diseases.
Karunas AS et al.·Biochem Genet
2021
Plasma circulating microRNAs associated with blood-based immune markers: a population-based study
Leonard S et al.·Clin Exp Immunol
2023
Evolutionary analyses of the gasdermin family suggest conserved roles in infection response despite loss of pore-forming functionality
Angosto-Bazarra D et al.·BMC Biol
2022Functional
Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis
Zhou Y et al.·Front Genet
2022
Epigenetic regulation of inflammation by microRNAs in post-infectious bronchiolitis obliterans
Duecker RP et al.·Clin Transl Immunology
2022
Assessment of Rare Genetic Variants to Identify Candidate Modifier Genes Underlying Neurological Manifestations in Neurofibromatosis 1 Patients
Tang J et al.·Genes (Basel)
2022Cohort
Functional analysis of a putative HER2-associated expressed enhancer, Her2-Enhancer1, in breast cancer cells
Rojhannezhad M et al.·Sci Rep
2023Functional
Top 10 full-text resultsSearch PubTator3 ↗
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools