OR2L13

olfactory receptor family 2 subfamily L member 13, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:248095183-248101163

Previous symbols: [ "OR2L14" ]

Links

ENSG00000196071 ∙ NCBI:284521 ∙ ∙ HGNC:19578 ∙ Uniprot:Q8N349 ∙ 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 OR2L13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2L13 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			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	0	0

Variants in OR2L13

This is a list of pathogenic ClinVar variants found in the OR2L13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248099428-C-T		not specified	Uncertain significance (Sep 15, 2021)
1-248099458-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-248099466-A-G		not specified	Uncertain significance (Apr 20, 2023)
1-248099469-C-T		not specified	Uncertain significance (Dec 20, 2023)
1-248099514-C-G		not specified	Uncertain significance (Feb 22, 2023)
1-248099514-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-248099542-C-A		not specified	Uncertain significance (Sep 23, 2023)
1-248099622-A-C		not specified	Uncertain significance (Sep 28, 2021)
1-248099634-G-A		not specified	Uncertain significance (May 20, 2024)
1-248099634-G-T		not specified	Uncertain significance (Jan 08, 2024)
1-248099656-T-A		not specified	Uncertain significance (May 18, 2022)
1-248099681-C-A		not specified	Uncertain significance (Mar 21, 2024)
1-248099722-C-G		not specified	Uncertain significance (Apr 28, 2022)
1-248099736-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-248099764-A-G		not specified	Uncertain significance (Dec 17, 2023)
1-248099778-A-G		not specified	Uncertain significance (Sep 18, 2023)
1-248099788-T-C		not specified	Uncertain significance (Jun 21, 2023)
1-248099860-C-T		not specified	Uncertain significance (Mar 07, 2023)
1-248099931-C-T		not specified	Uncertain significance (Jul 27, 2022)
1-248099953-T-G		not specified	Uncertain significance (Feb 23, 2023)
1-248099980-C-T		not specified	Uncertain significance (Jun 10, 2022)
1-248100028-G-T		not specified	Uncertain significance (Mar 25, 2024)
1-248100031-G-A		not specified	Uncertain significance (Jan 23, 2023)
1-248100132-C-T		not specified	Uncertain significance (Nov 28, 2023)
1-248100154-G-A		not specified	Uncertain significance (May 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2L13	protein_coding	protein_coding	ENST00000366478	1	163732

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000983	0.604	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.236	180	171	1.05	0.00000918	2056
Missense in Polyphen		42	50.252	0.83579		694
Synonymous	-1.58	82	65.7	1.25	0.00000380	636
Loss of Function	0.522	5	6.43	0.778	3.59e-7	85

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000148	0.000148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.000163	0.000163
South Asian	0.000229	0.000229
Other	0.000163	0.000163

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)

Recessive Scores

• pRec: 0.0885

Intolerance Scores

• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.146
• ghis: 0.442

Essentials

• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.281

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr168

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;biological_process;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;protein binding