OR3A1

olfactory receptor family 3 subfamily A member 1, the group of Olfactory receptors, family 3

Basic information

Region (hg38): 17:3291017-3298360

Links

ENSG00000180090 ∙ NCBI:4994 ∙ ∙ HGNC:8282 ∙ Uniprot:P47881 ∙ 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 OR3A1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OR3A1 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				1		1
missense			31	3	2	36
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	4	3

Variants in OR3A1

This is a list of pathogenic ClinVar variants found in the OR3A1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-3291715-G-C		not specified	Uncertain significance (Jul 28, 2021)
17-3291739-T-A		not specified	Uncertain significance (Feb 27, 2023)
17-3291739-T-C		not specified	Uncertain significance (Jun 28, 2022)
17-3291750-C-T		not specified	Uncertain significance (May 16, 2022)
17-3291754-C-A		not specified	Uncertain significance (Feb 15, 2023)
17-3291758-T-G		not specified	Uncertain significance (Oct 06, 2022)
17-3291759-T-C		not specified	Uncertain significance (Feb 10, 2022)
17-3291767-G-T		not specified	Uncertain significance (Dec 06, 2021)
17-3291781-T-C		not specified	Likely benign (Dec 21, 2022)
17-3291807-A-G		not specified	Uncertain significance (Jun 18, 2021)
17-3291829-C-A		not specified	Uncertain significance (Oct 22, 2021)
17-3291888-C-T		not specified	Uncertain significance (Mar 28, 2024)
17-3291898-G-C		not specified	Uncertain significance (Dec 18, 2023)
17-3291988-C-G		not specified	Uncertain significance (Dec 17, 2021)
17-3292005-G-C		not specified	Uncertain significance (Jan 08, 2024)
17-3292019-G-C		not specified	Uncertain significance (Sep 17, 2021)
17-3292042-A-G			Benign (Aug 02, 2017)
17-3292050-T-C		not specified	Uncertain significance (Dec 06, 2022)
17-3292057-C-T		not specified	Uncertain significance (Jun 17, 2024)
17-3292059-T-C			Benign (Aug 02, 2017)
17-3292110-T-C		not specified	Uncertain significance (Mar 11, 2022)
17-3292118-A-G			Likely benign (Sep 01, 2022)
17-3292146-A-G		not specified	Uncertain significance (Feb 28, 2023)
17-3292160-C-G		not specified	Uncertain significance (Nov 13, 2023)
17-3292173-G-T		not specified	Uncertain significance (Oct 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OR3A1	protein_coding	protein_coding	ENST00000323404	1	948

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0231	0.782	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.975	213	177	1.21	0.00000973	2027
Missense in Polyphen		42	39.841	1.0542		585
Synonymous	-0.331	77	73.4	1.05	0.00000405	699
Loss of Function	0.945	3	5.36	0.560	3.64e-7	53

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);GPCRs, Other;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: 0.122

Intolerance Scores

• loftool: 0.861
• rvis_EVS: 1.66
• rvis_percentile_EVS: 96.28

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.130

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Olfr411

Gene ontology

• Biological process: signal transduction;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