OR3A2

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

Basic information

Region (hg38): 17:3276177-3386317

Links

ENSG00000221882 ∙ NCBI:4995 ∙ ∙ HGNC:8283 ∙ Uniprot:P47893 ∙ 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 OR3A2 gene.

• Inborn genetic diseases (38 variants)
• not provided (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR3A2 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			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			19	4	3	26
Total	0	0	36	4	3

Variants in OR3A2

This is a list of pathogenic ClinVar variants found in the OR3A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3278050-G-A		not specified	Uncertain significance (Oct 04, 2022)
17-3278074-T-C		not specified	Uncertain significance (Oct 03, 2022)
17-3278097-T-C		not specified	Uncertain significance (Apr 29, 2024)
17-3278109-G-C		not specified	Uncertain significance (Dec 07, 2021)
17-3278110-C-T		not specified	Uncertain significance (Jan 22, 2024)
17-3278143-T-C		not specified	Uncertain significance (Aug 16, 2021)
17-3278170-C-T		not specified	Uncertain significance (Jul 14, 2023)
17-3278208-C-T		not specified	Uncertain significance (Jun 16, 2024)
17-3278211-C-G		not specified	Uncertain significance (Jul 06, 2021)
17-3278224-G-A		not specified	Uncertain significance (Oct 03, 2023)
17-3278236-C-T		not specified	Uncertain significance (May 05, 2023)
17-3278281-G-A		not specified	Uncertain significance (Dec 28, 2022)
17-3278305-C-T		not specified	Uncertain significance (Feb 13, 2024)
17-3278340-G-A		not specified	Uncertain significance (Sep 26, 2023)
17-3278386-T-C		not specified	Uncertain significance (Nov 07, 2023)
17-3278415-G-A		not specified	Uncertain significance (Mar 01, 2023)
17-3278418-G-A		not specified	Uncertain significance (Aug 15, 2023)
17-3278424-G-A		not specified	Uncertain significance (Nov 01, 2022)
17-3278505-C-T		not specified	Uncertain significance (Apr 25, 2022)
17-3278506-G-A		not specified	Uncertain significance (Jul 06, 2021)
17-3278533-T-C		not specified	Uncertain significance (Apr 12, 2022)
17-3278568-A-C		not specified	Uncertain significance (Dec 27, 2023)
17-3278658-C-T		not specified	Uncertain significance (Dec 03, 2021)
17-3278707-C-G		not specified	Uncertain significance (Aug 01, 2022)
17-3278749-T-C		not specified	Uncertain significance (Oct 28, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR3A2	protein_coding	protein_coding	ENST00000408891	1	1076

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000230	0.530	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.528	183	164	1.12	0.00000854	2058
Missense in Polyphen		30	31.634	0.94835		479
Synonymous	-0.447	74	69.3	1.07	0.00000396	704
Loss of Function	0.445	6	7.30	0.822	5.82e-7	77

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)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.740
• rvis_EVS: 1.28
• rvis_percentile_EVS: 93.77

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.255

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.122

Gene Damage Prediction

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

Gene ontology

• Biological process: signal transduction;G protein-coupled receptor signaling pathway;sensory perception of chemical stimulus;detection of chemical stimulus involved in sensory perception of smell
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;olfactory receptor activity;signaling receptor activity