LCN2

lipocalin 2, the group of Lipocalins

Basic information

Region (hg38): 9:128149071-128153453

Links

ENSG00000148346 ∙ NCBI:3934 ∙ OMIM:600181 ∙ HGNC:6526 ∙ Uniprot:P80188 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (25 variants)
• not_provided (6 variants)

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. These statistics are base on transcript: NM_000005564.5. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				1		1
missense			24	2	1	27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			6			6
Total	0	0	30	3	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN2	protein_coding	protein_coding	ENST00000373017	6	4385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.14e-9	0.0522	125653	0	94	125747	0.000374

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.431	122	109	1.12	0.00000592	1292
Missense in Polyphen		28	25.769	1.0866		332
Synonymous	0.957	41	49.6	0.827	0.00000303	384
Loss of Function	-0.350	13	11.7	1.11	5.84e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00395	0.00395
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000792	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000326	0.000326

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

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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