OR3A1

Summary

OR3A1 (olfactory receptor family 3 subfamily A member 1, HGNC:8282) is a protein-coding gene on chromosome 17p13.3, encoding Olfactory receptor 3A1 (P47881). Odorant receptor.

Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome.

Source: NCBI Gene 4994 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 77 total — 1 pathogenic
• Phenotypes (HPO): 1
• MANE Select transcript: NM_002550

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8282
Approved symbol	OR3A1
Name	olfactory receptor family 3 subfamily A member 1
Location	17p13.3
Locus type	gene with protein product
Status	Approved
Aliases	OLFRA03, OR40, OR17-40
Ensembl gene	ENSG00000180090
Ensembl biotype	protein_coding
Entrez	4994

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000323404

RefSeq mRNA: 1 — MANE Select: NM_002550 NM_002550

CCDS: CCDS11023

Canonical transcript exons

ENST00000323404 — 2 exons

Exon	Start	End
ENSE00001245019	3291017	3292588
ENSE00003813666	3298283	3298360

Expression profiles

Bgee: expression breadth broad, 14 present calls, max score 78.98.

Top tissues by expression

220 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.98	gold quality
secondary oocyte	CL:0000655	73.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.25	gold quality
oocyte	CL:0000023	62.54	silver quality
vena cava	UBERON:0004087	55.17	gold quality
lateral globus pallidus	UBERON:0002476	54.20	gold quality
Brodmann (1909) area 46	UBERON:0006483	49.14	gold quality
islet of Langerhans	UBERON:0000006	44.45	gold quality
buccal mucosa cell	CL:0002336	44.11	gold quality
saphenous vein	UBERON:0007318	44.05	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
subthalamic nucleus	UBERON:0001906	43.30	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	42.87	gold quality
substantia nigra pars compacta	UBERON:0001965	42.58	gold quality
substantia nigra pars reticulata	UBERON:0001966	42.39	gold quality
adult organism	UBERON:0007023	42.38	gold quality
colonic epithelium	UBERON:0000397	41.67	gold quality
biceps brachii	UBERON:0001507	41.44	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
dorsal plus ventral thalamus	UBERON:0001897	41.36	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
globus pallidus	UBERON:0001875	41.24	gold quality
ventral tegmental area	UBERON:0002691	41.17	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
ventricular zone	UBERON:0003053	40.56	silver quality
medulla oblongata	UBERON:0001896	40.54	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	2.95

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• This unique mechanism of continuous internalization and recycling of OR17-40 might be instrumental in allowing rapid recovery of odor perception. (PMID:16980412)
• This work shows the feasibility of an olfactory biosensor based on the immobilization of Saccharomyces cerevisiae yeast cells genetically modified to express the human olfactory receptor OR17-40 (PMID:17579849)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Or3a1	ENSMUSG00000063116
mus_musculus	Or3a1c	ENSMUSG00000070379
mus_musculus	Or3a1b	ENSMUSG00000070380
rattus_norvegicus	Or3a1f	ENSRNOG00000071441
rattus_norvegicus	Or3a1	ENSRNOG00000072302
rattus_norvegicus	Or3a1e	ENSRNOG00000086043

Paralogs (130): OR1I1 (ENSG00000094661), OR12D3 (ENSG00000112462), OR7A10 (ENSG00000127515), OR7C2 (ENSG00000127529), OR7C1 (ENSG00000127530), OR1E2 (ENSG00000127780), OR1J1 (ENSG00000136834), OR1L4 (ENSG00000136939), OR4D1 (ENSG00000141194), OR4K1 (ENSG00000155249), OR3A3 (ENSG00000159961), OR7G1 (ENSG00000161807), OR1Q1 (ENSG00000165202), OR1K1 (ENSG00000165204), OR4K2 (ENSG00000165762), OR4D6 (ENSG00000166884), OR1F1 (ENSG00000168124), OR4K14 (ENSG00000169484), OR4K15 (ENSG00000169488), OR7G3 (ENSG00000170920), OR7G2 (ENSG00000170923), OR1M1 (ENSG00000170929), OR4D5 (ENSG00000171014), OR1L6 (ENSG00000171459), OR1L3 (ENSG00000171481), OR1L8 (ENSG00000171496), OR1N2 (ENSG00000171501), OR1N1 (ENSG00000171505), OR2AT4 (ENSG00000171561), OR1A1 (ENSG00000172146), OR1A2 (ENSG00000172150), OR4C11 (ENSG00000172188), OR4X2 (ENSG00000172208), OR4D9 (ENSG00000172742), OR10K1 (ENSG00000173285), OR1L1 (ENSG00000173679), OR7D4 (ENSG00000174667), OR4S2 (ENSG00000174982), OR4B1 (ENSG00000175619), OR4D11 (ENSG00000176200)

Protein

Protein identifiers

Olfactory receptor 3A1 — P47881 (reviewed: P47881)

Alternative names: Olfactory receptor 17-40, Olfactory receptor OR17-15

All UniProt accessions (2): P47881, A0A126GVP1

UniProt curated annotations — full annotation on UniProt →

Function. Odorant receptor.

Subcellular location. Cell membrane.

Similarity. Belongs to the G-protein coupled receptor 1 family.

RefSeq proteins (1): NP_002541* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000276	GPCR_Rhodpsn	Family
IPR000725	Olfact_rcpt	Family
IPR017452	GPCR_Rhodpsn_7TM	Domain

Pfam: PF13853

UniProt features (21 total): topological domain 8, transmembrane region 7, sequence variant 2, chain 1, glycosylation site 1, disulfide bond 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P47881-F1	87.02	0.59

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Disulfide bonds (1): 100–192

Glycosylation sites (1): 8

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-381753	Olfactory Signaling Pathway
R-HSA-9752946	Expression and translocation of olfactory receptors

MSigDB gene sets: 35 (showing top): GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, KEGG_OLFACTORY_TRANSDUCTION, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, GOMF_OLFACTORY_RECEPTOR_ACTIVITY, GOMF_TRANSMEMBRANE_SIGNALING_RECEPTOR_ACTIVITY, GOMF_G_PROTEIN_COUPLED_RECEPTOR_ACTIVITY, GOBP_SENSORY_PERCEPTION_OF_SMELL, GOBP_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY, GOBP_DETECTION_OF_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION, GSE13485_DAY1_VS_DAY21_YF17D_VACCINE_PBMC_UP, WP_GPCRS_CLASS_A_RHODOPSINLIKE, WP_GPCRS_OTHER, REACTOME_OLFACTORY_SIGNALING_PATHWAY, MEF2C_TARGET_GENES

GO Biological Process (4): signal transduction (GO:0007165), G protein-coupled receptor signaling pathway (GO:0007186), sensory perception of smell (GO:0007608), detection of chemical stimulus involved in sensory perception of smell (GO:0050911)

GO Molecular Function (2): G protein-coupled receptor activity (GO:0004930), olfactory receptor activity (GO:0004984)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Sensory Perception	1
Olfactory Signaling Pathway	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transmembrane signaling receptor activity	2
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
G protein-coupled receptor activity	1
signal transduction	1
sensory perception of chemical stimulus	1
sensory perception of smell	1
detection of chemical stimulus involved in sensory perception	1
G protein-coupled receptor signaling pathway	1
detection of chemical stimulus involved in sensory perception of smell	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

264 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR3A1	KRTAP9-7	A8MTY7	595
OR3A1	KRTAP9-8	Q9BYQ0	507
OR3A1	KRTAP9-1	A8MXZ3	472
OR3A1	CNGA2	Q16280	449
OR3A1	TMEM95	Q3KNT9	430
OR3A1	TMEM220	Q6QAJ8	397
OR3A1	C17orf50	Q8WW18	392
OR3A1	TBC1D3K	A0A087X1G2	371
OR3A1	RHO	P08100	370
OR3A1	TMTC1	Q8IUR5	357
OR3A1	TMEM92	Q6UXU6	348
OR3A1	CDRT15L2	A8MXV6	348
OR3A1	CNGA4	Q8IV77	322
OR3A1	OMP	P47874	315
OR3A1	TBC1D3H	P0C7X1	306

IntAct

3 interactions, top by confidence:

A	B	Type	Score
MPDZ	OR3A1	psi-mi:“MI:0407”(direct interaction)	0.440
OR3A1	ALDH1A2	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (4): TCP10 (Affinity Capture-MS), ALDH1A2 (Affinity Capture-MS), TCP10L2 (Affinity Capture-MS), OR3A1 (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: A6NH00, O60403, O95371, O95918, P23266, P23267, P23275, P34984, P47881, P47888, P47893, Q15619, Q5JQS5, Q5TZ20, Q60885, Q60891, Q60894, Q6IEZ7, Q7Z3T1, Q8N628, Q8NG76, Q8NG77, Q8NG97, Q8NGA6, Q8NGC4, Q8NGE3, Q8NGE9, Q8NGQ2, Q8NGQ4, Q8NGR4, Q8NGS0, Q8NGT9, Q8NGX9, Q8NGY1, Q8NGZ6, Q8NH02, Q8NH03, Q8NH04, Q8NHB1, Q8VGD6

Diamond homologs: A3KFT3, A4D2G3, A6NF89, A6NND4, O43749, O60412, O76099, O76100, O95007, O95222, O95918, P0C7N1, P0C7N5, P0DN81, P23265, P23266, P23267, P23268, P23269, P23270, P23272, P23273, P30953, P34984, P34986, P47881, P47890, P58173, Q0VAX9, Q15619, Q15622, Q5JQS5, Q5TZ20, Q60879, Q60882, Q60886, Q6IFH4, Q7TRF3, Q8NG83, Q8NG98

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	68
Likely benign	5
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
523262	GRCh37/hg19 17p13.3-13.2(chr17:2339561-3447162)	Pathogenic

SpliceAI

359 predictions. Top by Δscore:

Variant	Effect	Δscore
17:3291761:AT:A	donor_gain	0.7800
17:3291811:CTG:C	donor_gain	0.7800
17:3291913:C:CT	acceptor_gain	0.7600
17:3292330:A:C	donor_gain	0.7600
17:3291810:CCT:C	donor_gain	0.7500
17:3291914:G:C	acceptor_gain	0.7500
17:3291807:ATACC:A	acceptor_loss	0.7300
17:3291808:TACCT:T	acceptor_loss	0.7300
17:3291809:ACCT:A	acceptor_loss	0.7300
17:3291810:CC:C	acceptor_loss	0.7300
17:3291811:CT:C	acceptor_loss	0.7300
17:3291812:T:G	acceptor_loss	0.7300
17:3292259:A:C	acceptor_gain	0.7300
17:3291812:TGA:T	donor_gain	0.7000
17:3291817:C:CT	acceptor_gain	0.6600
17:3291817:CA:C	acceptor_loss	0.6600
17:3291832:C:CT	donor_gain	0.6600
17:3291871:T:TA	donor_gain	0.6600
17:3291825:A:C	acceptor_loss	0.6300
17:3292256:C:CT	acceptor_gain	0.6300
17:3291823:A:C	acceptor_loss	0.6100
17:3291849:C:CT	donor_gain	0.6100
17:3291962:A:AC	donor_gain	0.6100
17:3291806:GATA:G	donor_loss	0.6000
17:3291810:C:G	donor_loss	0.6000
17:3291813:G:C	acceptor_loss	0.6000
17:3291830:A:AT	donor_gain	0.6000
17:3291969:A:AC	donor_gain	0.6000
17:3291970:C:CC	donor_gain	0.6000
17:3291762:T:TA	donor_gain	0.5800

AlphaMissense

2044 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:3292538:G:C	F15L	0.881
17:3292538:G:T	F15L	0.881
17:3292540:A:G	F15L	0.881
17:3292043:G:C	F180L	0.868
17:3292043:G:T	F180L	0.868
17:3292045:A:G	F180L	0.868
17:3292070:G:C	F171L	0.856
17:3292070:G:T	F171L	0.856
17:3292072:A:G	F171L	0.856
17:3292205:G:C	F126L	0.836
17:3292205:G:T	F126L	0.836
17:3292207:A:G	F126L	0.836
17:3291821:G:C	F254L	0.830
17:3291821:G:T	F254L	0.830
17:3291823:A:G	F254L	0.830
17:3292220:C:A	M121I	0.798
17:3292220:C:G	M121I	0.798
17:3292220:C:T	M121I	0.798
17:3292349:G:C	S78R	0.796
17:3292349:G:T	S78R	0.796
17:3292351:T:G	S78R	0.796
17:3291825:A:T	I253K	0.787
17:3291701:G:C	S294R	0.780
17:3291701:G:T	S294R	0.780
17:3291703:T:G	S294R	0.780
17:3292268:G:C	F105L	0.776
17:3292268:G:T	F105L	0.776
17:3292270:A:G	F105L	0.776
17:3292490:A:C	F31L	0.757
17:3292490:A:T	F31L	0.757

dbSNP variants (sampled 300 via entrez): RS1000503088 (17:3295266 T>A), RS1000633287 (17:3297045 G>A), RS1001301760 (17:3294081 G>T), RS1001584290 (17:3294356 AT>A), RS1001645376 (17:3294145 G>A), RS1002191775 (17:3295854 A>C), RS1002711308 (17:3295583 T>C), RS1002805626 (17:3299323 T>C), RS1002850047 (17:3292832 C>A,T), RS1003316439 (17:3293183 G>A), RS1003364781 (17:3299166 G>C), RS1003635547 (17:3291333 C>G,T), RS1003779384 (17:3298059 T>A), RS1004083608 (17:3296718 A>C), RS1004783263 (17:3296392 A>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:607432

GenCC curated gene-disease

Mondo (1): lissencephaly spectrum disorders (MONDO:0018838)

Orphanet (1): Lissencephaly (Orphanet:48471)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0001339	Lissencephaly

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST002142_13	Cocaine dependence	4.000000e-07
GCST002142_7	Cocaine dependence	2.000000e-06

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D054082	Lissencephaly	C10.500.507.450.499; C16.131.666.507.450.499

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases mutagenesis	1
Cadmium	decreases expression	1
Asbestos, Crocidolite	affects expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.