LACC1

Chr 13AR

laccase domain containing 1

Also known as: C13orf31, FAMIN, JUVAR

NCBI Gene: 144811ENSG00000179630UniProt: Q8IV20OMIM: 613409

This gene encodes a purine nucleoside enzyme that regulates innate immunity in macrophages by modulating purine nucleotide metabolism, promoting optimal NOD2-induced signaling, cytokine secretion, and bacterial clearance. Mutations cause autosomal recessive juvenile arthritis, along with other inflammatory conditions including early-onset Crohn's disease and systemic juvenile idiopathic arthritis. The gene shows low constraint against loss-of-function variants (pLI near 0), consistent with its recessive inheritance pattern.

OMIMResearchSummary from RefSeq, OMIM, UniProt
DNmechanismARLOEUF 1.081 OMIM phenotype
Clinical Summary— LACC1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
59 unique Pathogenic / Likely Pathogenic· 49 VUS of 128 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.08LOEUF
pLI 0.000
Z-score 1.35
OE 0.63 (0.39–1.08)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
1.64Z-score
OE missense 0.69 (0.61–0.79)
157 obs / 226.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.63 (0.39–1.08)
0≤0.351.4
Missense OE0.69 (0.61–0.79)
0≤0.61.4
Synonymous OE0.97
0≤1.21.6
LoF obs/exp: 10 / 15.8Missense obs/exp: 157 / 226.5Syn Z: 0.23
DN
0.6162th %ile
GOF
0.3887th %ile
LOF
0.3744th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

128 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic56
Likely Pathogenic3
VUS49
Likely Benign6
Benign4
Conflicting1
56
Pathogenic
3
Likely Pathogenic
49
VUS
6
Likely Benign
4
Benign
1
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
4
1
51
0
56
Likely Pathogenic
1
2
0
0
3
VUS
0
48
1
0
49
Likely Benign
0
4
0
2
6
Benign
0
2
0
2
4
Conflicting
—1
Total557524119

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

LACC1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients