LCN10

protein-coding

lipocalin 10, the group of Lipocalins

Gene summary

Members of the lipocalin family, such as LCN10, 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_001001712.3

Inheritance

—

ClinVar variants

U:34B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.76

Max pathogenic AF

—

Genomic locus

chr9:136,738,167-136,743,356

External References & Databases

Ensembl (ENSG00000187922)

Transcript & Mutation Effects

hg38 • Region Span ~5.2 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 LCN10 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001712.3. 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			31 clinvar	3 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar		1 clinvar	4
Total	0	0	34	3	1	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001001712.3	RefSeq	NP_001001712.2	6	MANE Select
ENST00000497771.6	Ensembl	ENSP00000418491.1	6	MANE Select
NM_001368089.1	RefSeq	NP_001355018.1	5	Standard
NM_001368090.1	RefSeq	NP_001355019.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

small molecule binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000497771
Coding exons: 6
Length: 5190
Individuals with no LoFs: 125128
Homozygous LoFs: 4
Heterozygous LoFs: 380
Defined: 125512
p: 0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.330	112	122	0.916	0.00000754	1263
Missense (PolyPhen)		31	36.79	0.84262		381
Synonymous	-1.40	71	57.5	1.24	0.00000382	414
Loss of Function	0.720	8	10.5	0.761	4.48e-7	119

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.014	0.014	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000081	0.000079	rare
South Asian	0.0033	0.0032	notable
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

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

Recessive Scores

pRec: 0.0869

Intolerance Scores

LoFtool: 0.682
RVIS EVS: 0.51
RVIS percentile EVS: 80.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.112

Gene Damage Prediction

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