LCN8

lipocalin 8, the group of Lipocalins

Basic information

Region (hg38): 9:136754386-136758543

Previous symbols: [ "LCN5" ]

Links

ENSG00000204001 ∙ NCBI:138307 ∙ OMIM:612902 ∙ HGNC:27038 ∙ Uniprot:Q6JVE9 ∙ 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 LCN8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN8 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						0
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	2	0

Variants in LCN8

This is a list of pathogenic ClinVar variants found in the LCN8 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136755267-C-T		not specified	Uncertain significance (Jun 18, 2024)
9-136755288-C-T		not specified	Uncertain significance (Feb 14, 2023)
9-136755309-C-T		not specified	Likely benign (Aug 09, 2021)
9-136755310-G-A		not specified	Uncertain significance (May 18, 2023)
9-136755444-C-T		not specified	Likely benign (Jun 12, 2023)
9-136755460-C-T		not specified	Uncertain significance (Dec 20, 2021)
9-136755462-C-T		not specified	Uncertain significance (Feb 23, 2023)
9-136755481-C-G		not specified	Uncertain significance (Dec 26, 2023)
9-136755506-C-G		not specified	Uncertain significance (Mar 23, 2022)
9-136756577-C-A		not specified	Uncertain significance (May 26, 2023)
9-136756583-G-C		not specified	Uncertain significance (Nov 13, 2023)
9-136756587-C-T		not specified	Uncertain significance (Sep 16, 2021)
9-136757045-A-T		not specified	Uncertain significance (May 11, 2022)
9-136757057-C-T		not specified	Uncertain significance (Nov 15, 2021)
9-136757072-C-T		not specified	Uncertain significance (Aug 26, 2022)
9-136757089-A-G		not specified	Uncertain significance (Mar 01, 2024)
9-136757107-G-A		not specified	Uncertain significance (Dec 21, 2023)
9-136757143-C-T		not specified	Uncertain significance (Mar 15, 2024)
9-136757158-A-G		not specified	Uncertain significance (May 20, 2024)
9-136757914-C-A		not specified	Likely benign (Apr 20, 2024)
9-136757914-C-T		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN8	protein_coding	protein_coding	ENST00000371688	7	3841

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000876	0.808	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0190	101	102	0.995	0.00000713	961
Missense in Polyphen		34	29.397	1.1566		314
Synonymous	0.135	41	42.1	0.974	0.00000294	298
Loss of Function	1.11	6	9.75	0.615	4.12e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000974	0.0000924
European (Non-Finnish)	0.0000802	0.0000791
Middle Eastern	0.0000547	0.0000544
South Asian	0.00151	0.00150
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in male fertility. May act as a retinoid carrier protein within the epididymis.

Intolerance Scores

• loftool: 0.621
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.29

Haploinsufficiency Scores

• pHI: 0.0368
• hipred: N
• hipred_score: 0.180
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.198

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcn8

Gene ontology

• Biological process: response to hormone
• Cellular component: extracellular region
• Molecular function: small molecule binding