LCN10

lipocalin 10, the group of Lipocalins

Basic information

Region (hg38): 9:136738167-136743356

Links

ENSG00000187922 ∙ NCBI:414332 ∙ OMIM:612904 ∙ HGNC:20892 ∙ Uniprot:Q6JVE6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LCN10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN10 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding						0
Total	0	0	16	1	1

Variants in LCN10

This is a list of pathogenic ClinVar variants found in the LCN10 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136739548-G-A		not specified	Likely benign (Jun 01, 2023)
9-136740024-T-C		not specified	Uncertain significance (Mar 15, 2024)
9-136740033-G-A		not specified	Uncertain significance (Dec 14, 2021)
9-136740038-A-C		not specified	Uncertain significance (Mar 22, 2023)
9-136740835-C-T			Benign (Mar 29, 2018)
9-136740865-G-A		not specified	Uncertain significance (Oct 30, 2023)
9-136740872-G-A		not specified	Uncertain significance (Jan 31, 2024)
9-136740881-G-A		not specified	Uncertain significance (Aug 21, 2023)
9-136741281-G-A		not specified	Uncertain significance (Mar 14, 2023)
9-136741308-G-A		not specified	Uncertain significance (Apr 25, 2022)
9-136741313-C-G		not specified	Uncertain significance (Feb 23, 2023)
9-136741891-C-T		not specified	Uncertain significance (Jan 19, 2022)
9-136741900-C-T		not specified	Uncertain significance (Jan 26, 2022)
9-136741902-C-T		not specified	Uncertain significance (Jun 06, 2023)
9-136741938-G-A		not specified	Uncertain significance (Dec 03, 2021)
9-136741965-G-A		not specified	Uncertain significance (Mar 29, 2023)
9-136742002-T-A		not specified	Uncertain significance (Nov 06, 2023)
9-136742828-C-T		not specified	Uncertain significance (Feb 17, 2022)
9-136742885-C-T		not specified	Uncertain significance (Mar 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN10	protein_coding	protein_coding	ENST00000497771	6	5190

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000308	0.577	125128	4	380	125512	0.00153

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.330	112	122	0.916	0.00000754	1263
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000791	0.000790
Ashkenazi Jewish	0.00	0.00
East Asian	0.0143	0.0142
Finnish	0.00	0.00
European (Non-Finnish)	0.0000810	0.0000794
Middle Eastern	0.0143	0.0142
South Asian	0.00325	0.00321
Other	0.000164	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0934
• hipred: N
• hipred_score: 0.180

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.112

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcn10

Gene ontology

• Cellular component: extracellular region
• Molecular function: small molecule binding