LCN9

protein-coding

lipocalin 9, the group of Lipocalins

Gene summary

Members of the lipocalin family, such as LCN9, have a common structure consisting of an 8-stranded antiparallel beta-barrel that forms a cup-shaped ligand-binding pocket or calyx. Lipocalins generally bind small hydrophobic ligands and transport them to specific cells (Suzuki et al., 2004 [PubMed 15363845]).[supplied by OMIM, Aug 2009]

MANE transcript

NM_001393661.1

Inheritance

—

ClinVar variants

U:18B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.53

Max pathogenic AF

—

Genomic locus

chr9:135,663,309-135,666,961

External References & Databases

Ensembl (ENSG00000148386)

Transcript & Mutation Effects

hg38 • Region Span ~3.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LCN9 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 21

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001393661.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar	3 clinvar		21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	3	0	21

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001393661.1	RefSeq	NP_001380590.1	5	MANE Select
ENST00000619315.2	Ensembl	ENSP00000482296.2	5	MANE Select
ENST00000277526.8	Ensembl	ENSP00000277526.4	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Transport of fatty acids
Transport of vitamins, nucleosides, and related molecules
SLC-mediated transmembrane transport
Transport of small molecules

Molecular Function

small molecule binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000277526
Coding exons: 7
Length: 3101
Individuals with no LoFs: 124421
Homozygous LoFs: 1
Heterozygous LoFs: 239
Defined: 124661
p: 0.000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0975	108	105	1.03	0.00000633	1144
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00065	0.00065	rare
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.010	0.0098	notable
Finnish	0.000052	0.000046	rare
European (Non-Finnish)	0.000090	0.000088	rare
South Asian	0.00014	0.00013	rare
Other	0.00017	0.00017	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0915

Intolerance Scores

RVIS EVS: 0.26
RVIS percentile EVS: 70.26

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0111

Gene Damage Prediction

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