OR2L2

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

Basic information

Region (hg38): 1:248030070-248042305

Previous symbols: [ "OR2L4P", "OR2L12" ]

Links

ENSG00000203663 ∙ NCBI:26246 ∙ ∙ HGNC:8266 ∙ Uniprot:Q8NH16 ∙ 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 OR2L2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2L2 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	2	0

Variants in OR2L2

This is a list of pathogenic ClinVar variants found in the OR2L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-248038325-T-C		not specified	Uncertain significance (Apr 26, 2023)
1-248038329-G-A		not specified	Uncertain significance (Jul 05, 2023)
1-248038331-A-T		not specified	Uncertain significance (Dec 08, 2023)
1-248038356-T-C		not specified	Uncertain significance (Jul 08, 2022)
1-248038436-C-T		not specified	Uncertain significance (Jul 27, 2023)
1-248038484-A-C		not specified	Uncertain significance (Jun 27, 2022)
1-248038493-A-G		not specified	Uncertain significance (Nov 21, 2022)
1-248038499-C-A		not specified	Uncertain significance (May 02, 2024)
1-248038512-A-G		not specified	Uncertain significance (Jun 16, 2024)
1-248038574-T-G		not specified	Uncertain significance (Apr 07, 2023)
1-248038589-G-A		not specified	Uncertain significance (Mar 29, 2022)
1-248038635-T-C		not specified	Uncertain significance (Jun 03, 2024)
1-248038672-A-G		not specified	Likely benign (Dec 19, 2022)
1-248038675-C-A		not specified	Uncertain significance (Dec 19, 2022)
1-248038706-T-C		not specified	Uncertain significance (Mar 29, 2022)
1-248038766-T-C		not specified	Uncertain significance (Aug 05, 2023)
1-248038808-C-T		not specified	Uncertain significance (Feb 02, 2022)
1-248038917-A-G		not specified	Uncertain significance (Feb 17, 2022)
1-248038949-C-A		not specified	Uncertain significance (Jun 07, 2024)
1-248039007-T-C		not specified	Uncertain significance (Jun 18, 2024)
1-248039045-C-T		not specified	Uncertain significance (May 11, 2022)
1-248039077-C-A		not specified	Uncertain significance (Aug 16, 2021)
1-248039081-A-G		not specified	Likely benign (Dec 13, 2023)
1-248039093-T-G		not specified	Uncertain significance (Oct 03, 2022)
1-248039153-G-A		not specified	Uncertain significance (Jul 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2L2	protein_coding	protein_coding	ENST00000366479	1	1134

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	-1.45	213	161	1.32	0.00000811	2035
Missense in Polyphen		38	29.343	1.295		464
Synonymous	-1.60	74	58.4	1.27	0.00000273	633
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: 0.0868

Intolerance Scores

• loftool: 0.809
• rvis_EVS: 1.02
• rvis_percentile_EVS: 90.98

Haploinsufficiency Scores

• pHI: 0.0850
• hipred: N
• hipred_score: 0.112
• ghis: 0.397

Essentials

• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

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