LCN9

lipocalin 9, the group of Lipocalins

Basic information

Region (hg38): 9:135663309-135666961

Links

ENSG00000148386 ∙ NCBI:392399 ∙ OMIM:612903 ∙ HGNC:17442 ∙ Uniprot:Q8WX39 ∙ 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 LCN9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN9 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in LCN9

This is a list of pathogenic ClinVar variants found in the LCN9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-135663347-G-A		not specified	Uncertain significance (Nov 10, 2022)
9-135663358-A-G		not specified	Likely benign (Apr 27, 2024)
9-135663361-G-A		not specified	Uncertain significance (Apr 07, 2023)
9-135663364-G-T		not specified	Uncertain significance (Nov 20, 2023)
9-135663365-C-T		not specified	Uncertain significance (May 03, 2023)
9-135663372-G-T		not specified	Uncertain significance (Jan 05, 2022)
9-135664190-T-C		not specified	Uncertain significance (Nov 21, 2023)
9-135664211-G-C		not specified	Uncertain significance (Jan 10, 2023)
9-135664247-G-A		not specified	Uncertain significance (Feb 28, 2024)
9-135664723-G-A		not specified	Uncertain significance (Dec 09, 2023)
9-135664741-G-A		not specified	Uncertain significance (Sep 06, 2023)
9-135664750-G-A		not specified	Likely benign (Oct 20, 2021)
9-135665341-C-A		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN9	protein_coding	protein_coding	ENST00000277526	7	3101

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00170	0.901	124421	1	239	124661	0.000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0975	108	105	1.03	0.00000633	1144
Missense in Polyphen		24	28.374	0.84584		384
Synonymous	-1.04	55	46.0	1.20	0.00000344	313
Loss of Function	1.45	6	11.2	0.535	5.76e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00174	0.00173
Ashkenazi Jewish	0.0000996	0.0000993
East Asian	0.00997	0.00984
Finnish	0.0000524	0.0000464
European (Non-Finnish)	0.0000896	0.0000885
Middle Eastern	0.00997	0.00984
South Asian	0.000136	0.000131
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0915

Intolerance Scores

• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.26

Haploinsufficiency Scores

• pHI: 0.0574
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0111

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcn9

Gene ontology

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