LCNL1

Chr 9

lipocalin like 1

NCBI Gene: 401562ENSG00000214402UniProt: Q6ZST4

LCNL1 encodes a protein predicted to bind small molecules, though its specific physiological function remains unclear. The gene shows low constraint against loss-of-function variants (pLI 0.001, LOEUF 1.88), and no established disease associations have been reported in the literature. Further research is needed to determine if LCNL1 variants cause human disease.

ResearchSummary from RefSeq
MultiplemechanismLOEUF 1.88
Clinical Summary— LCNL1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
83 unique Pathogenic / Likely Pathogenic· 34 VUS of 124 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
1.88LOEUF
pLI 0.001
Z-score -0.25
OE 1.15 (0.53–1.88)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.74Z-score
OE missense 0.78 (0.64–0.95)
67 obs / 86.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE1.15 (0.53–1.88)
0≤0.351.4
Missense OE0.78 (0.64–0.95)
0≤0.61.4
Synonymous OE0.96
0≤1.21.6
LoF obs/exp: 4 / 3.5Missense obs/exp: 67 / 86.3Syn Z: 0.20
DN
0.6648th %ile
GOF
0.73top 25%
LOF
0.2289th %ile

This gene has evidence for multiple mechanisms of pathogenicity (gain-of-function and dominant-negative). Both the Badonyi & Marsh prediction and the broader genomic evidence point to gain-of-function as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

GOFprediction above median
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

124 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic79
Likely Pathogenic4
VUS34
Likely Benign4
Conflicting2
79
Pathogenic
4
Likely Pathogenic
34
VUS
4
Likely Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
79
0
79
Likely Pathogenic
0
0
4
0
4
VUS
0
26
8
0
34
Likely Benign
0
4
0
0
4
Benign
0
0
0
0
0
Conflicting
—2
Total030910123

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

View in ClinVar →

Protein Context — Lollipop Plot

LCNL1 · 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
Proteome Profiling of Canine Epididymal Fluid: In Search of Protein Markers of Epididymal Sperm Motility
Cichowska AW et al.·Int J Mol Sci
2023
Mendelian randomization analysis identified genes pleiotropically associated with central corneal thickness
Yang Z et al.·BMC Genomics
2021
The G Protein-Coupled Receptor-Related Gene Signatures for Diagnosis and Prognosis in Glioblastoma: A Deep Learning Model Using RNA-Seq Data
Khalili-Tanha G et al.·Asian Pac J Cancer Prev
2024Functional
Genomic stratification based on microenvironment immune types and PD-L1 for tailoring therapeutic strategies in bladder cancer
Lyu X et al.·BMC Cancer
2021
Proteomic Analysis of Intracellular and Membrane-Associated Fractions of Canine (Canis lupus familiaris) Epididymal Spermatozoa and Sperm Structure Separation
Zmudzinska A et al.·Animals (Basel)
2022
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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