LCN1

lipocalin 1, the group of Lipocalins

Basic information

Region (hg38): 9:135521438-135526540

Links

ENSG00000160349 ∙ NCBI:3933 ∙ OMIM:151675 ∙ HGNC:6525 ∙ Uniprot:P31025 ∙ 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 LCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN1 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	1	2
missense			12	2	1	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	3	2

Variants in LCN1

This is a list of pathogenic ClinVar variants found in the LCN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135521522-A-T		not specified	Uncertain significance (Apr 15, 2024)
9-135522078-C-T		not specified	Uncertain significance (Mar 04, 2024)
9-135522118-G-A			Likely benign (Apr 01, 2022)
9-135522140-C-G		not specified	Uncertain significance (Feb 13, 2024)
9-135522141-T-A		not specified	Uncertain significance (Oct 25, 2023)
9-135522143-G-C		not specified	Uncertain significance (Dec 15, 2023)
9-135523243-G-A		not specified	Likely benign (Dec 15, 2022)
9-135523297-C-T		not specified	Uncertain significance (Mar 16, 2024)
9-135523884-G-A			Benign (Aug 08, 2018)
9-135523885-G-C			Benign (Aug 08, 2018)
9-135523886-G-A		not specified	Uncertain significance (Mar 28, 2024)
9-135523918-G-T		not specified	Uncertain significance (Sep 20, 2023)
9-135523957-C-T		not specified	Uncertain significance (Oct 30, 2023)
9-135523987-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-135524841-A-G		not specified	Likely benign (Feb 15, 2023)
9-135524880-G-A		not specified	Uncertain significance (Nov 30, 2021)
9-135524889-C-T		not specified	Uncertain significance (May 09, 2023)
9-135524890-G-A		not specified	Uncertain significance (Jun 24, 2022)
9-135524925-C-G		not specified	Uncertain significance (Dec 13, 2021)
9-135525152-G-A		not specified	Uncertain significance (Nov 10, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN1	protein_coding	protein_coding	ENST00000263598	6	5095

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.33e-8	0.0596	125660	0	71	125731	0.000282

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.763	130	108	1.21	0.00000683	1120
Missense in Polyphen		25	21.718	1.1511		308
Synonymous	0.142	47	48.3	0.974	0.00000368	339
Loss of Function	-0.583	11	9.10	1.21	4.70e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000633	0.000633
Ashkenazi Jewish	0.00	0.00
East Asian	0.000576	0.000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000376	0.000369
Middle Eastern	0.000576	0.000544
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Could play a role in taste reception. Could be necessary for the concentration and delivery of sapid molecules in the gustatory system. Can bind various ligands, with chemical structures ranging from lipids and retinoids to the macrocyclic antibiotic rifampicin and even to microbial siderophores. Exhibits an extremely wide ligand pocket.
• Pathway: Transport of fatty acids;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.820
• rvis_EVS: 0.22
• rvis_percentile_EVS: 68.27

Haploinsufficiency Scores

• pHI: 0.0276
• hipred: N
• hipred_score: 0.112
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.682

Gene Damage Prediction

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

Gene ontology

• Biological process: retina homeostasis;proteolysis;negative regulation of endopeptidase activity;long-chain fatty acid transport;response to stimulus;sensory perception of taste
• Cellular component: extracellular region;extracellular space
• Molecular function: cysteine-type endopeptidase inhibitor activity;signaling receptor binding;zinc ion binding;chloride ion binding;small molecule binding