OR2D2

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

Basic information

Region (hg38): 11:6891574-6892500

Previous symbols: [ "OR2D1" ]

Links

ENSG00000166368 ∙ NCBI:120776 ∙ OMIM:608494 ∙ HGNC:8244 ∙ Uniprot:Q9H210 ∙ 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 OR2D2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2D2 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			31	1		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	1	0

Variants in OR2D2

This is a list of pathogenic ClinVar variants found in the OR2D2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6891591-T-C		not specified	Uncertain significance (Dec 06, 2023)
11-6891596-A-G		not specified	Uncertain significance (Sep 16, 2021)
11-6891612-C-A		not specified	Uncertain significance (Feb 28, 2024)
11-6891655-C-T		not specified	Uncertain significance (Nov 07, 2024)
11-6891662-G-C		not specified	Uncertain significance (Nov 08, 2024)
11-6891834-C-T		not specified	Uncertain significance (Jun 19, 2024)
11-6891849-A-G		not specified	Uncertain significance (Jun 05, 2023)
11-6891854-A-G		not specified	Uncertain significance (Apr 17, 2024)
11-6891891-C-T		not specified	Uncertain significance (Sep 29, 2023)
11-6891900-G-A		not specified	Uncertain significance (Dec 27, 2024)
11-6891909-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-6891912-T-G		not specified	Uncertain significance (Jul 09, 2021)
11-6891981-T-G		not specified	Uncertain significance (Jan 20, 2023)
11-6892054-C-A		not specified	Uncertain significance (Sep 01, 2021)
11-6892071-G-C		not specified	Uncertain significance (Sep 02, 2024)
11-6892072-C-G		not specified	Uncertain significance (Aug 17, 2021)
11-6892115-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-6892137-G-C		not specified	Uncertain significance (Feb 20, 2025)
11-6892179-C-G		not specified	Uncertain significance (Mar 08, 2025)
11-6892185-T-G		not specified	Uncertain significance (Aug 10, 2021)
11-6892261-C-A		not specified	Uncertain significance (Jan 17, 2024)
11-6892262-T-C		not specified	Uncertain significance (Mar 06, 2025)
11-6892272-T-C		not specified	Uncertain significance (Feb 19, 2025)
11-6892278-T-C		not specified	Uncertain significance (Feb 02, 2022)
11-6892296-C-T		not specified	Uncertain significance (Mar 01, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2D2	protein_coding	protein_coding	ENST00000299459	1	1110

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.02e-8	0.0594	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.946	202	168	1.21	0.00000821	1980
Missense in Polyphen		54	39.633	1.3625		540
Synonymous	-1.25	79	66.0	1.20	0.00000325	683
Loss of Function	-0.783	10	7.66	1.31	4.77e-7	80

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;GPCRs, Class A Rhodopsin-like;Signaling by GPCR;Signal Transduction;Olfactory Signaling Pathway;G alpha (s) signalling events;GPCR downstream signalling (Consensus)

Intolerance Scores

• loftool: 0.917
• rvis_EVS: 2.18
• rvis_percentile_EVS: 98.07

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr715

Gene ontology

• Biological process: G protein-coupled receptor signaling pathway;sensory perception of smell;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