OR52L1

olfactory receptor family 52 subfamily L member 1, the group of Olfactory receptors, family 52

Basic information

Region (hg38): 11:5985892-5986985

Links

ENSG00000183313 ∙ NCBI:338751 ∙ ∙ HGNC:14785 ∙ Uniprot:Q8NGH7 ∙ 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 OR52L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR52L1 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			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in OR52L1

This is a list of pathogenic ClinVar variants found in the OR52L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-5985993-T-C		not specified	Uncertain significance (Mar 30, 2024)
11-5986020-G-A		not specified	Uncertain significance (May 27, 2022)
11-5986029-A-G		not specified	Uncertain significance (Sep 29, 2022)
11-5986056-A-T		not specified	Uncertain significance (Apr 12, 2022)
11-5986089-C-A		not specified	Uncertain significance (Oct 03, 2022)
11-5986089-C-T		not specified	Likely benign (Aug 09, 2021)
11-5986122-T-C		not specified	Uncertain significance (Aug 26, 2022)
11-5986124-G-T		not specified	Uncertain significance (Mar 11, 2024)
11-5986144-T-C		not specified	Likely benign (Jan 30, 2024)
11-5986294-T-A		not specified	Uncertain significance (Dec 20, 2023)
11-5986303-T-C		not specified	Uncertain significance (Jan 18, 2022)
11-5986357-T-C		not specified	Uncertain significance (Jul 16, 2021)
11-5986369-G-C		not specified	Uncertain significance (Aug 15, 2023)
11-5986552-A-G		not specified	Uncertain significance (Mar 20, 2024)
11-5986566-A-G		not specified	Uncertain significance (Jun 18, 2021)
11-5986587-C-A		not specified	Uncertain significance (Jul 25, 2023)
11-5986611-G-A		not specified	Uncertain significance (Feb 27, 2024)
11-5986629-G-A		not specified	Uncertain significance (Jul 19, 2023)
11-5986629-G-T		not specified	Uncertain significance (May 01, 2024)
11-5986636-C-T		not specified	Uncertain significance (Jan 19, 2024)
11-5986657-C-G		not specified	Uncertain significance (Oct 10, 2023)
11-5986700-C-T		not specified	Uncertain significance (Mar 01, 2024)
11-5986719-G-A		not specified	Uncertain significance (Aug 02, 2022)
11-5986729-A-G		not specified	Uncertain significance (Mar 08, 2024)
11-5986811-T-G		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR52L1	protein_coding	protein_coding	ENST00000332249	1	1094

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000187	0.278	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.350	189	176	1.07	0.00000852	2108
Missense in Polyphen		54	60.373	0.89445		763
Synonymous	-1.45	86	70.5	1.22	0.00000345	722
Loss of Function	-0.0965	7	6.73	1.04	4.41e-7	75

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Odorant receptor. {ECO:0000305}.
• Pathway: Olfactory transduction - Homo sapiens (human);Olfactory receptor activity;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.694
• rvis_EVS: 1.64
• rvis_percentile_EVS: 96.17

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.144

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0930

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr685

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity