LCN12

lipocalin 12, the group of Lipocalins

Basic information

Region (hg38): 9:136949550-136955497

Links

ENSG00000184925

∙ NCBI:286256 ∙ OMIM:612905 ∙ HGNC:28733 ∙ Uniprot:Q6JVE5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCN12 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN12 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			6 clinvar	2 clinvar		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	2	0

Variants in LCN12

This is a list of pathogenic ClinVar variants found in the LCN12 region.

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

Position	Phenotype	Significance	ClinVar
9-136952401-T-G	not specified	Uncertain significance (Feb 03, 2022)	2210845
9-136952923-C-T	not specified	Uncertain significance (Oct 12, 2022)	2210345
9-136952941-C-T	not specified	Uncertain significance (Dec 21, 2023)	3118117
9-136952973-G-A	not specified	Uncertain significance (Feb 03, 2022)	2275281
9-136952994-G-A	not specified	Likely benign (Oct 06, 2021)	3118118
9-136953019-C-T	not specified	Uncertain significance (Sep 16, 2021)	2375116
9-136953875-G-A	not specified	Likely benign (Dec 21, 2021)	2373182
9-136953896-C-T	not specified	Uncertain significance (Apr 12, 2022)	2219563
9-136954181-C-T	not specified	Uncertain significance (Mar 18, 2024)	3290292

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN12	protein_coding	protein_coding	ENST00000371633	6	5947

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000146	0.674	124590	1	165	124756	0.000666

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.610	96	114	0.840	0.00000699	1213
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000277	0.000276
Ashkenazi Jewish	0.00230	0.00229
East Asian	0.0000557	0.0000556
Finnish	0.0000942	0.0000928
European (Non-Finnish)	0.000331	0.000327
Middle Eastern	0.0000557	0.0000556
South Asian	0.00304	0.00301
Other	0.000665	0.000660

dbNSFP

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

Recessive Scores

pRec: 0.0832

Intolerance Scores

loftool: 0.566
rvis_EVS: 0.44
rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

pHI: 0.0617
hipred: N
hipred_score: 0.112
ghis: 0.417

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0870

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Lcn12
Phenotype

Gene ontology

Biological process: long-chain fatty acid transport
Cellular component: extracellular region
Molecular function: retinoic acid binding