LCN6

protein-coding

lipocalin 6, the group of Lipocalins|MicroRNA protein coding host genes

Gene summary

Predicted to enable small molecule binding activity. Predicted to be involved in single fertilization. Predicted to act upstream of or within several processes, including acrosome reaction; calcium ion homeostasis; and response to calcium ion. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198946.3

Inheritance

—

ClinVar variants

U:32B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr9:136,744,017-136,748,525

External References & Databases

Ensembl (ENSG00000267206)

Transcript & Mutation Effects

hg38 • Region Span ~4.5 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 LCN6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198946.3. 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					1 clinvar	1
missense			31 clinvar	4 clinvar	1 clinvar	36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	32	4	2	38

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198946.3	RefSeq	NP_945184.1	5	MANE Select
ENST00000341206.9	Ensembl	ENSP00000339621.3	5	MANE Select
ENST00000476567.1	Ensembl	ENSP00000468337.1	3	Standard
ENST00000960388.1	Ensembl	ENSP00000630447.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

single fertilization

Molecular Function

small molecule binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341206
Coding exons: 5
Length: 4518
Individuals with no LoFs: 125690
Homozygous LoFs: 1
Heterozygous LoFs: 46
Defined: 125737
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.239	106	99.3	1.07	0.00000599	1037
Missense (PolyPhen)		22	27.3	0.80587		346
Synonymous	-0.989	55	46.4	1.18	0.00000320	338
Loss of Function	0.525	8	9.77	0.819	5.01e-7	98

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00019	0.00018	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0.00043	0.00042	rare
European (Non-Finnish)	0.00019	0.00019	rare
South Asian	0.00037	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in male fertility.;

Recessive Scores

pRec: 0.0797

Intolerance Scores

LoFtool: 0.791
RVIS EVS: 0.51
RVIS percentile EVS: 80.01

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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