LCN2

lipocalin 2, the group of Lipocalins

Basic information

Region (hg38): 9:128149071-128153453

Links

ENSG00000148346NCBI:3934OMIM:600181HGNC:6526Uniprot:P80188AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCN2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
1
missense
13
clinvar
1
clinvar
1
clinvar
15
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
2
2
non coding
1
clinvar
1
clinvar
2
Total 0 0 13 3 2

Variants in LCN2

This is a list of pathogenic ClinVar variants found in the LCN2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
9-128149536-G-A not specified Uncertain significance (Feb 28, 2023)2456995
9-128149544-T-C not specified Uncertain significance (Nov 22, 2022)2329267
9-128149551-G-T Likely benign (Dec 12, 2017)780048
9-128149569-C-A not specified Uncertain significance (Feb 08, 2023)2469138
9-128149598-T-A not specified Uncertain significance (May 24, 2023)2551675
9-128149618-A-G Likely benign (Jun 20, 2018)753120
9-128149655-G-A not specified Uncertain significance (Nov 10, 2022)2239112
9-128150229-C-A Likely benign (Aug 14, 2018)707849
9-128150254-A-G not specified Uncertain significance (Oct 20, 2023)3118124
9-128150300-C-A not specified Uncertain significance (Aug 16, 2022)2307141
9-128150310-A-C not specified Uncertain significance (May 10, 2024)3290300
9-128150320-C-T not specified Uncertain significance (Jan 30, 2024)3118125
9-128151664-G-C not specified Uncertain significance (Apr 04, 2024)3290298
9-128151690-G-A not specified Uncertain significance (Nov 16, 2021)2387042
9-128151725-T-C Benign (Aug 07, 2018)731724
9-128151891-C-G not specified Benign (Mar 29, 2016)403029
9-128151903-C-A Benign (Aug 07, 2018)731725
9-128151921-C-T Benign (Aug 07, 2018)731726
9-128151969-T-C not specified Uncertain significance (Mar 28, 2024)3290297
9-128152204-C-T not specified Uncertain significance (Apr 17, 2024)3290296
9-128152233-T-C not specified Uncertain significance (Apr 07, 2023)2535343
9-128152245-G-A not specified Uncertain significance (May 06, 2024)3290299
9-128152276-T-A not specified Uncertain significance (Nov 18, 2022)2219462
9-128152283-C-G not specified Uncertain significance (Dec 16, 2023)3118126
9-128153111-G-A not specified Uncertain significance (Jul 14, 2022)2210643

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
LCN2protein_codingprotein_codingENST00000373017 64385
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.14e-90.05221256530941257470.000374
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4311221091.120.000005921292
Missense in Polyphen2825.7691.0866332
Synonymous0.9574149.60.8270.00000303384
Loss of Function-0.3501311.71.115.84e-7128

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.003950.00395
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0001390.000139
European (Non-Finnish)0.00007920.0000615
Middle Eastern0.00005440.0000544
South Asian0.00006540.0000653
Other0.0003260.000326

dbNSFP

Source: dbNSFP

Function
FUNCTION: Iron-trafficking protein involved in multiple processes such as apoptosis, innate immunity and renal development. Binds iron through association with 2,5-dihydroxybenzoic acid (2,5- DHBA), a siderophore that shares structural similarities with bacterial enterobactin, and delivers or removes iron from the cell, depending on the context. Iron-bound form (holo-24p3) is internalized following binding to the SLC22A17 (24p3R) receptor, leading to release of iron and subsequent increase of intracellular iron concentration. In contrast, association of the iron-free form (apo-24p3) with the SLC22A17 (24p3R) receptor is followed by association with an intracellular siderophore, iron chelation and iron transfer to the extracellular medium, thereby reducing intracellular iron concentration. Involved in apoptosis due to interleukin-3 (IL3) deprivation: iron-loaded form increases intracellular iron concentration without promoting apoptosis, while iron-free form decreases intracellular iron levels, inducing expression of the proapoptotic protein BCL2L11/BIM, resulting in apoptosis. Involved in innate immunity, possibly by sequestrating iron, leading to limit bacterial growth. {ECO:0000269|PubMed:12453413}.;
Pathway
IL-17 signaling pathway - Homo sapiens (human);Interleukin-4 and 13 signaling;Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System;Transport of small molecules;Iron uptake and transport;Metal sequestration by antimicrobial proteins (Consensus)

Recessive Scores

pRec
0.647

Intolerance Scores

loftool
0.730
rvis_EVS
0.84
rvis_percentile_EVS
88.23

Haploinsufficiency Scores

pHI
0.310
hipred
N
hipred_score
0.112
ghis

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.978

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Lcn2
Phenotype
homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; growth/size/body region phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); renal/urinary system phenotype; immune system phenotype; liver/biliary system phenotype;

Gene ontology

Biological process
cellular iron ion homeostasis;response to virus;response to herbicide;response to mycotoxin;positive regulation of gene expression;siderophore transport;cytokine-mediated signaling pathway;antimicrobial humoral response;positive regulation of cell projection organization;cellular response to nutrient levels;defense response to bacterium;neutrophil degranulation;innate immune response;protein homotrimerization;cellular response to hydrogen peroxide;cellular response to lipopolysaccharide;cellular response to interleukin-1;cellular response to tumor necrosis factor;extrinsic apoptotic signaling pathway in absence of ligand;sequestering of iron ion;positive regulation of cold-induced thermogenesis
Cellular component
extracellular region;extracellular space;cytosol;specific granule lumen;extracellular exosome
Molecular function
protease binding;iron ion binding;small molecule binding;protein homodimerization activity;enterobactin binding