LCN12

protein-coding

lipocalin 12, the group of Lipocalins

Gene summary

Members of the lipocalin family, such as LCN12, 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_178536.4

Inheritance

—

ClinVar variants

U:35B:5

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.71

Max pathogenic AF

—

Genomic locus

chr9:136,949,551-136,955,497

External References & Databases

Ensembl (ENSG00000184925)

Transcript & Mutation Effects

hg38 • Region Span ~5.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LCN12 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178536.4. 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			32 clinvar	4 clinvar		36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	35	5	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178536.4	RefSeq	NP_848631.2	6	MANE Select
ENST00000371633.8	Ensembl	ENSP00000360696.3	6	MANE Select
ENST00000371632.7	Ensembl	ENSP00000360695.3	4	Standard
ENST00000471615.6	Ensembl	ENSP00000473473.1	4	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

Biological Process

long-chain fatty acid transport

Molecular Function

retinoic acid binding

Cellular Component

extracellular region

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000371633
Coding exons: 6
Length: 5947
Individuals with no LoFs: 124590
Homozygous LoFs: 1
Heterozygous LoFs: 165
Defined: 124756
p: 0.000666

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.610	96	114	0.840	0.00000699	1213
Missense (PolyPhen)		23	35.855	0.64148		431
Synonymous	-0.643	62	55.9	1.11	0.00000401	378
Loss of Function	0.843	7	9.86	0.710	4.89e-7	97

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.00015	0.00014	rare
Ashkenazi Jewish	0.0023	0.0023	notable
East Asian	0.000056	0.000056	rare
Finnish	0.000094	0.000093	rare
European (Non-Finnish)	0.00033	0.00033	rare
South Asian	0.0030	0.0030	notable
Other	0.00066	0.00066	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds all-trans retinoic acid and may act as a retinoid carrier protein within the epididymis. May play a role in male fertility (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0832

Intolerance Scores

LoFtool: 0.566
RVIS EVS: 0.44
RVIS percentile EVS: 77.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0870

Gene Damage Prediction

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