LCN15

lipocalin 15, the group of Lipocalins

Basic information

Region (hg38): 9:136759634-136766255

Links

ENSG00000177984 ∙ NCBI:389812 ∙ ∙ HGNC:33777 ∙ Uniprot:Q6UWW0 ∙ 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 LCN15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN15 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			7	4		11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	4	0

Variants in LCN15

This is a list of pathogenic ClinVar variants found in the LCN15 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136761826-G-A		not specified	Uncertain significance (Jan 17, 2023)
9-136762230-G-C		not specified	Likely benign (Sep 29, 2023)
9-136763403-G-C		not specified	Uncertain significance (Aug 04, 2023)
9-136763436-G-C		not specified	Uncertain significance (Dec 08, 2023)
9-136763871-C-T		not specified	Likely benign (Apr 12, 2023)
9-136763873-G-A		not specified	Likely benign (Jul 26, 2021)
9-136763970-A-C		not specified	Uncertain significance (Dec 07, 2021)
9-136763991-C-T		not specified	Uncertain significance (Apr 26, 2023)
9-136764430-G-A		not specified	Uncertain significance (May 16, 2022)
9-136764445-G-A		not specified	Likely benign (Aug 17, 2022)
9-136764445-G-T		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN15	protein_coding	protein_coding	ENST00000316144	6	6622

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00417	0.874	125682	0	42	125724	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.412	92	104	0.886	0.00000584	1184
Missense in Polyphen		35	33.899	1.0325		394
Synonymous	-0.932	54	46.0	1.18	0.00000303	348
Loss of Function	1.31	5	9.31	0.537	3.95e-7	116

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000739	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000157	0.000149
Middle Eastern	0.000739	0.000653
South Asian	0.000469	0.000359
Other	0.000188	0.000163

dbNSFP

Source: dbNSFP

• Pathway: Transport of fatty acids;Transport of vitamins, nucleosides, and related molecules;SLC-mediated transmembrane transport;Transport of small molecules (Consensus)

Intolerance Scores

• loftool: 0.714
• rvis_EVS: 0.48
• rvis_percentile_EVS: 79.25

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0298

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcn15

Gene ontology

• Cellular component: extracellular region
• Molecular function: small molecule binding