LCN10

Chr 9

lipocalin 10

NCBI Gene: 414332ENSG00000187922UniProt: Q6JVE6OMIM: 612904

LCN10 encodes a lipocalin family protein that binds and transports small hydrophobic ligands, potentially serving as a retinoid carrier protein in the epididymis with a possible role in male fertility. The gene is not constrained against loss-of-function variants and no established Mendelian diseases have been associated with LCN10 mutations in the provided data.

OMIMResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.37
Clinical Summary— LCN10
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
71 unique Pathogenic / Likely Pathogenic· 38 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
1.37LOEUF
pLI 0.000
Z-score 0.72
OE 0.76 (0.45–1.37)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.33Z-score
OE missense 0.92 (0.79–1.07)
112 obs / 122.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.76 (0.45–1.37)
0≤0.351.4
Missense OE0.92 (0.79–1.07)
0≤0.61.4
Synonymous OE1.24
0≤1.21.6
LoF obs/exp: 8 / 10.5Missense obs/exp: 112 / 122.3Syn Z: -1.40
DN
0.6550th %ile
GOF
0.74top 25%
LOF
0.2581th %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

128 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic68
Likely Pathogenic3
VUS38
Likely Benign3
Benign2
Conflicting2
68
Pathogenic
3
Likely Pathogenic
38
VUS
3
Likely Benign
2
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
68
0
68
Likely Pathogenic
0
0
3
0
3
VUS
0
31
7
0
38
Likely Benign
0
3
0
0
3
Benign
1
0
1
0
2
Conflicting
—2
Total134790116

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

View in ClinVar →

Protein Context — Lollipop Plot

LCN10 · 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 →

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