LCN6

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

Basic information

Region (hg38): 9:136744017-136748525

Links

ENSG00000267206 ∙ NCBI:158062 ∙ OMIM:609379 ∙ HGNC:17337 ∙ Uniprot:P62502 ∙ 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 LCN6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCN6 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					1	1
missense			15	1	1	17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	2

Variants in LCN6

This is a list of pathogenic ClinVar variants found in the LCN6 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136744696-T-C		not specified	Uncertain significance (Sep 20, 2023)
9-136745175-A-G		not specified	Uncertain significance (Jul 12, 2023)
9-136745261-G-C			Benign (Jan 25, 2018)
9-136745263-G-T		not specified	Uncertain significance (Aug 01, 2022)
9-136745272-C-T		not specified	Uncertain significance (Aug 14, 2023)
9-136745852-T-A		not specified	Uncertain significance (Jan 23, 2024)
9-136745853-C-T		not specified	Uncertain significance (Jan 23, 2024)
9-136745859-C-G		not specified	Uncertain significance (Sep 28, 2021)
9-136745865-C-T		not specified	Uncertain significance (Dec 27, 2023)
9-136745891-A-G		not specified	Uncertain significance (Oct 21, 2021)
9-136747425-C-T		not specified	Likely benign (Jul 08, 2022)
9-136747481-C-T			Benign (Jan 25, 2018)
9-136747485-C-T		not specified	Uncertain significance (Aug 02, 2021)
9-136747492-C-A		not specified	Uncertain significance (Jul 26, 2022)
9-136747548-A-G		not specified	Uncertain significance (Feb 27, 2023)
9-136747562-A-G		not specified	Uncertain significance (Nov 05, 2021)
9-136748471-G-C		not specified	Uncertain significance (Apr 17, 2023)
9-136748480-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCN6	protein_coding	protein_coding	ENST00000341206	5	4518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000193	0.477	125690	1	46	125737	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.239	106	99.3	1.07	0.00000599	1037
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000185	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.000425	0.000416
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000163	0.000163
South Asian	0.000365	0.000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0630
• hipred: N
• hipred_score: 0.146

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Lcn6
• Phenotype: reproductive system phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: single fertilization
• Cellular component: extracellular region
• Molecular function: small molecule binding