OR2L3

olfactory receptor family 2 subfamily L member 3, the group of Olfactory receptors, family 2

Basic information

Region (hg38): 1:248046836-248063407

Links

ENSG00000198128 ∙ NCBI:391192 ∙ ∙ HGNC:15009 ∙ Uniprot:Q8NG85 ∙ 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 OR2L3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2L3 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in OR2L3

This is a list of pathogenic ClinVar variants found in the OR2L3 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248060763-A-G		not specified	Uncertain significance (Sep 16, 2021)
1-248060943-A-G		not specified	Uncertain significance (Jul 19, 2023)
1-248060961-A-G		not specified	Uncertain significance (Apr 15, 2024)
1-248061003-G-A		not specified	Uncertain significance (Jun 27, 2023)
1-248061018-C-T		not specified	Uncertain significance (Mar 23, 2022)
1-248061030-A-G		not specified	Uncertain significance (Sep 14, 2022)
1-248061040-A-G		not specified	Uncertain significance (Jun 01, 2023)
1-248061082-G-A		not specified	Uncertain significance (Jun 04, 2024)
1-248061136-C-T		not specified	Uncertain significance (Jul 16, 2021)
1-248061274-T-A		not specified	Uncertain significance (Oct 26, 2022)
1-248061334-G-T		not specified	Uncertain significance (Jul 19, 2022)
1-248061336-C-T		not specified	Uncertain significance (May 04, 2023)
1-248061343-T-C		not specified	Uncertain significance (Dec 27, 2022)
1-248061435-G-A		not specified	Uncertain significance (Dec 15, 2022)
1-248061459-C-T		not specified	Uncertain significance (Jun 08, 2022)
1-248061488-G-C		not specified	Uncertain significance (Jun 10, 2022)
1-248061517-C-T		not specified	Likely benign (Mar 28, 2023)
1-248061528-A-G		not specified	Uncertain significance (Oct 05, 2023)
1-248061564-G-A		not specified	Uncertain significance (Dec 20, 2023)
1-248061568-T-A		not specified	Uncertain significance (May 24, 2023)
1-248061610-G-T		not specified	Likely benign (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2L3	protein_coding	protein_coding	ENST00000359959	1	939

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.27	203	158	1.29	0.00000804	2022
Missense in Polyphen		34	29.252	1.1623		472
Synonymous	-0.365	63	59.4	1.06	0.00000290	642
Loss of Function

LoF frequencies by population

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

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: 0.0931

Intolerance Scores

• loftool: 0.852
• rvis_EVS: 1.13
• rvis_percentile_EVS: 92.19

Haploinsufficiency Scores

• pHI: 0.0459
• hipred: N
• hipred_score: 0.112
• ghis: 0.396

Essentials

• 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

• 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: molecular_function;G protein-coupled receptor activity;olfactory receptor activity