LCNL1

lipocalin like 1

Basic information

Region (hg38): 9:136981904-136986410

Links

ENSG00000214402 ∙ NCBI:401562 ∙ ∙ HGNC:34436 ∙ Uniprot:Q6ZST4 ∙ 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 LCNL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LCNL1 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			13	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	3	0

Variants in LCNL1

This is a list of pathogenic ClinVar variants found in the LCNL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-136983662-A-T		not specified	Uncertain significance (May 09, 2023)
9-136983663-C-A		not specified	Uncertain significance (Aug 17, 2022)
9-136983699-G-T		not specified	Uncertain significance (Jan 09, 2024)
9-136984500-G-A		not specified	Likely benign (Apr 05, 2023)
9-136984530-G-A		not specified	Likely benign (Sep 08, 2024)
9-136984543-C-T		not specified	Uncertain significance (Apr 04, 2023)
9-136984734-G-A		not specified	Uncertain significance (Aug 02, 2023)
9-136984740-C-T		not specified	Likely benign (Oct 26, 2021)
9-136984752-A-G		not specified	Uncertain significance (Feb 09, 2023)
9-136984764-C-T		not specified	Uncertain significance (Feb 15, 2023)
9-136984783-G-T		not specified	Uncertain significance (Nov 21, 2023)
9-136984836-C-T		not specified	Uncertain significance (Jun 26, 2024)
9-136984842-G-A		not specified	Uncertain significance (Apr 15, 2024)
9-136984851-G-A		not specified	Uncertain significance (Aug 05, 2024)
9-136984859-C-T		not specified	Uncertain significance (Aug 22, 2023)
9-136984949-C-T		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LCNL1	protein_coding	protein_coding	ENST00000408973	3	4507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00114	0.405	124717	0	67	124784	0.000269

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.738	67	86.3	0.776	0.00000493	1020
Missense in Polyphen		19	19.769	0.96109		274
Synonymous	0.195	37	38.5	0.960	0.00000230	351
Loss of Function	-0.251	4	3.49	1.15	2.47e-7	38

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00112	0.00112
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000239	0.000238
Middle Eastern	0.000167	0.000167
South Asian	0.00	0.00
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.663
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.153
• ghis: 0.411

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

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

Gene ontology

• Molecular function: small molecule binding