LCN1
Chr 9lipocalin 1
Also known as: PMFA, TLC, TP, VEGP
The protein binds and transports various hydrophobic ligands including lipids and retinoids, serves as the primary lipid binding protein in tears, and may function in taste reception by concentrating sapid molecules in the gustatory system. Based on the extremely low pLI score and high LOEUF score, LCN1 appears highly tolerant to loss-of-function variants, and no definitive disease associations have been established for this gene. The predicted dominant negative mechanism suggests potential pathogenicity through protein interference rather than simple loss of function.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly tolerant — LoF variants common in population
Tolerant to missense variation
The highest-scoring mechanism for this gene is dominant-negative.
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
115 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 54 | 0 | 54 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 2 | 36 | 12 | 0 | 50 |
Likely Benign | 0 | 2 | 0 | 1 | 3 |
Benign | 0 | 1 | 0 | 1 | 2 |
Conflicting | — | 1 | |||
| Total | 2 | 39 | 68 | 2 | 112 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
LCN1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
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