OR2D3

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

Basic information

Region (hg38): 11:6921002-6921994

Links

ENSG00000178358 ∙ NCBI:120775 ∙ ∙ HGNC:15146 ∙ Uniprot:Q8NGH3 ∙ 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 OR2D3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR2D3 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in OR2D3

This is a list of pathogenic ClinVar variants found in the OR2D3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-6921006-G-T		not specified	Uncertain significance (Jun 19, 2024)
11-6921032-A-G		not specified	Uncertain significance (Jan 29, 2024)
11-6921088-C-G		not specified	Uncertain significance (Oct 27, 2023)
11-6921107-G-C		not specified	Uncertain significance (Aug 31, 2022)
11-6921125-C-A		not specified	Uncertain significance (Apr 01, 2024)
11-6921143-C-T		not specified	Likely benign (Jul 14, 2024)
11-6921155-C-G		not specified	Uncertain significance (Dec 07, 2021)
11-6921210-G-A		not specified	Likely benign (Sep 30, 2024)
11-6921287-C-A		not specified	Uncertain significance (Feb 03, 2022)
11-6921315-G-A		not specified	Uncertain significance (Dec 27, 2022)
11-6921332-T-C		not specified	Uncertain significance (Jun 10, 2022)
11-6921387-C-T		not specified	Uncertain significance (Jan 09, 2024)
11-6921419-G-A		not specified	Uncertain significance (Oct 17, 2023)
11-6921450-C-T		not specified	Uncertain significance (Oct 04, 2022)
11-6921480-T-C		not specified	Uncertain significance (Oct 20, 2024)
11-6921528-C-G		not specified	Uncertain significance (Dec 01, 2022)
11-6921544-T-A		not specified	Likely benign (Mar 22, 2023)
11-6921612-C-G		not specified	Uncertain significance (Aug 14, 2024)
11-6921642-C-T		not specified	Uncertain significance (Jan 04, 2024)
11-6921645-T-C		not specified	Uncertain significance (Nov 16, 2021)
11-6921653-A-G		not specified	Uncertain significance (Jan 09, 2024)
11-6921655-G-A		not specified	Uncertain significance (Jul 26, 2024)
11-6921659-G-A		not specified	Uncertain significance (Jan 09, 2024)
11-6921684-C-T			Benign (Jul 01, 2024)
11-6921743-G-A		not specified	Uncertain significance (Dec 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR2D3	protein_coding	protein_coding	ENST00000317834	1	1060

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00841	0.809	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.343	184	171	1.07	0.00000810	2146
Missense in Polyphen		45	37.797	1.1906		539
Synonymous	-1.23	78	65.4	1.19	0.00000306	682
Loss of Function	1.04	4	6.98	0.573	2.93e-7	91

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)

Recessive Scores

• pRec: 0.0728

Intolerance Scores

• loftool: 0.825
• rvis_EVS: 1.11
• rvis_percentile_EVS: 92.04

Haploinsufficiency Scores

• pHI: 0.0778
• hipred: N
• hipred_score: 0.170

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.134

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr709-ps1

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