OR56A3

Summary

OR56A3 (olfactory receptor family 56 subfamily A member 3, HGNC:14786) is a protein-coding gene on chromosome 11p15.4, encoding Olfactory receptor 56A3 (Q8NH54). 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 390083 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 159 total
• MANE Select transcript: NM_001003443

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14786
Approved symbol	OR56A3
Name	olfactory receptor family 56 subfamily A member 3
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000184478
Ensembl biotype	protein_coding
Entrez	390083

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding_CDS_not_defined, 2 protein_coding

ENST00000528915, ENST00000641160, ENST00000641878, ENST00000641905

RefSeq mRNA: 1 — MANE Select: NM_001003443 NM_001003443

CCDS: CCDS41614

Canonical transcript exons

ENST00000641160 — 3 exons

Exon	Start	End
ENSE00003812147	5947311	5951347
ENSE00003812782	5944806	5945082
ENSE00003812883	5942251	5942374

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 76.25.

Top tissues by expression

106 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	76.25	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	46.92	silver quality
granulocyte	CL:0000094	41.81	silver quality
bone marrow cell	CL:0002092	41.14	gold quality
cortical plate	UBERON:0005343	40.78	silver quality
placenta	UBERON:0001987	39.71	gold quality
testis	UBERON:0000473	38.94	gold quality
left testis	UBERON:0004533	38.36	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
right testis	UBERON:0004534	36.87	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
bone marrow	UBERON:0002371	34.29	gold quality
monocyte	CL:0000576	33.48	silver quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
islet of Langerhans	UBERON:0000006	31.15	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
prefrontal cortex	UBERON:0000451	30.85	silver quality
tonsil	UBERON:0002372	30.55	gold quality
primary visual cortex	UBERON:0002436	30.05	gold quality
liver	UBERON:0002107	29.94	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
duodenum	UBERON:0002114	28.14	gold quality
blood	UBERON:0000178	27.61	gold quality
lymph node	UBERON:0000029	27.57	gold quality
superior frontal gyrus	UBERON:0002661	27.17	gold quality
pancreas	UBERON:0001264	27.12	silver quality
calcaneal tendon	UBERON:0003701	27.05	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-CURD-11	yes	93.17
E-ANND-3	yes	4.58

Regulation

Is transcription factor: no

Cross-species orthologs

7 orthologs

Organism	Symbol	Gene ID
danio_rerio	adra1ab	ENSDARG00000027638
danio_rerio	adra2db	ENSDARG00000054667
danio_rerio	adra2da	ENSDARG00000091277
mus_musculus	Or56a3b	ENSMUSG00000095248
mus_musculus	Or56a3	ENSMUSG00000096029
rattus_norvegicus	Or56a3b	ENSRNOG00000077271
caenorhabditis_elegans	ser-5	WBGENE00008890

Paralogs (18): ADRB1 (ENSG00000043591), ADRA1A (ENSG00000120907), DRD2 (ENSG00000149295), ADRA2A (ENSG00000150594), GPR101 (ENSG00000165370), ADRB2 (ENSG00000169252), ADRA1B (ENSG00000170214), ADRA1D (ENSG00000171873), OR5T3 (ENSG00000172489), OR56A1 (ENSG00000180934), OR5T1 (ENSG00000181698), OR5T2 (ENSG00000181718), OR56A4 (ENSG00000183389), ADRA2C (ENSG00000184160), OR13F1 (ENSG00000186881), OR56A5 (ENSG00000188691), ADRB3 (ENSG00000188778), ADRA2B (ENSG00000274286)

Protein

Protein identifiers

Olfactory receptor 56A3 — Q8NH54 (reviewed: Q8NH54)

Alternative names: Olfactory receptor 56A6

All UniProt accessions (2): Q8NH54, A0A126GWL6

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_001003443* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000276	GPCR_Rhodpsn	Family
IPR000725	Olfact_rcpt	Family
IPR017452	GPCR_Rhodpsn_7TM	Domain
IPR050402	OR51/52/56-like	Family

Pfam: PF13853

UniProt features (20 total): topological domain 8, transmembrane region 7, glycosylation site 2, chain 1, disulfide bond 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NH54-F1	85.20	0.49

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): 101–193

Glycosylation sites (2): 6, 185

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 18 (showing top): GOBP_CELLULAR_RESPONSE_TO_LIPID, GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, GOBP_RESPONSE_TO_LIPID, 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, REACTOME_OLFACTORY_SIGNALING_PATHWAY, REACTOME_SENSORY_PERCEPTION, GOBP_DETECTION_OF_CHEMICAL_STIMULUS

GO Biological Process (6): cellular response to lipid (GO:0071396), system process (GO:0003008), 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 (3): G protein-coupled receptor activity (GO:0004930), olfactory receptor activity (GO:0004984), signaling receptor activity (GO:0038023)

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

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Olfactory Signaling Pathway	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transmembrane signaling receptor activity	2
response to lipid	1
cellular response to chemical stimulus	1
multicellular organismal process	1
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
molecular transducer activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

118 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR56A3	KRTAP19-8	Q3LI54	621
OR56A3	KRTAP5-7	Q6L8G8	515
OR56A3	CNGA4	Q8IV77	483
OR56A3	GPR87	Q9BY21	459
OR56A3	KRTAP5-11	Q6L8G4	447
OR56A3	KRTAP5-5	Q701N2	446
OR56A3	TMEM184A	Q6ZMB5	445
OR56A3	GPR171	O14626	437
OR56A3	KCNAB3	O43448	358
OR56A3	RIBC2	Q9H4K1	348
OR56A3	FIGN	Q5HY92	326
OR56A3	P2RY13	Q9BPV8	305
OR56A3	P2RY14	Q15391	294
OR56A3	SMC1B	Q8NDV3	275
OR56A3	CHKB	Q9Y259	273

IntAct

2 interactions, top by confidence:

A	B	Type	Score
OR56A3	H2AC4	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (1): OR56A3 (Proximity Label-MS)

ESM2 similar proteins: A0A3B3IT45, A6NMU1, A6NND4, O88628, P0C7T3, Q6W049, Q8NGF0, Q8NGF1, Q8NGF3, Q8NGH5, Q8NGH6, Q8NGH7, Q8NGH8, Q8NGH9, Q8NGI0, Q8NGI1, Q8NGI2, Q8NGI3, Q8NGJ4, Q8NGJ8, Q8NGJ9, Q8NGK2, Q8NGK3, Q8NGK4, Q8NGK6, Q8NGU1, Q8NGW6, Q8NGY3, Q8NH53, Q8NH54, Q8NH55, Q8NH56, Q8NH57, Q8NH60, Q8NH61, Q8NH63, Q8NH67, Q8NH76, Q8TCB6, Q8VBV9

Diamond homologs: A0A3B3IT45, A4D2G3, A6NF89, A6NGY5, A6NL08, A6NL26, A6NMU1, A6NND4, O88628, P0C629, P0C646, P0C7N1, P0C7T3, P23266, P23273, P23274, P30954, Q13606, Q60888, Q62007, Q6IF63, Q6IFG1, Q6W049, Q8NGA6, Q8NGF0, Q8NGF1, Q8NGF3, Q8NGG8, Q8NGH5, Q8NGH6, Q8NGH7, Q8NGH8, Q8NGH9, Q8NGI0, Q8NGI1, Q8NGI2, Q8NGI3, Q8NGI7, Q8NGJ2, Q8NGJ3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	151
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

261 predictions. Top by Δscore:

Variant	Effect	Δscore
11:5947658:GAT:G	donor_gain	0.9000
11:5947628:GCCCA:G	donor_gain	0.8100
11:5947780:T:TA	donor_gain	0.8000
11:5947781:A:AA	donor_gain	0.8000
11:5947724:T:G	donor_gain	0.7900
11:5947688:G:GT	donor_gain	0.7800
11:5947660:T:G	donor_gain	0.7000
11:5947751:A:G	donor_gain	0.6700
11:5947981:GA:G	donor_gain	0.6700
11:5947977:C:G	donor_gain	0.6600
11:5947380:G:GT	donor_gain	0.6500
11:5947658:G:GT	donor_gain	0.6500
11:5947601:C:A	donor_gain	0.6400
11:5947963:G:GT	donor_gain	0.6400
11:5947384:C:G	donor_gain	0.6300
11:5947867:G:GT	donor_gain	0.6200
11:5947709:C:A	donor_gain	0.6000
11:5947708:TC:T	donor_gain	0.5900
11:5948082:G:GA	donor_gain	0.5700
11:5947600:TCCTG:T	donor_gain	0.5600
11:5947620:G:GT	donor_gain	0.5500
11:5948012:C:G	acceptor_gain	0.5500
11:5947538:C:CG	donor_gain	0.5400
11:5947614:T:A	donor_gain	0.5400
11:5947618:T:A	donor_gain	0.5400
11:5947710:A:AG	donor_gain	0.5300
11:5947819:T:G	donor_gain	0.5300
11:5947665:A:G	donor_gain	0.5200
11:5947783:TC:T	donor_gain	0.5200
11:5947810:GAAAT:G	donor_gain	0.5200

AlphaMissense

2061 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:5947392:T:C	F16L	0.918
11:5947394:C:A	F16L	0.918
11:5947394:C:G	F16L	0.918
11:5948112:A:C	S256R	0.915
11:5948114:C:A	S256R	0.915
11:5948114:C:G	S256R	0.915
11:5947452:A:C	S36R	0.909
11:5947454:C:A	S36R	0.909
11:5947454:C:G	S36R	0.909
11:5948109:T:C	F255L	0.877
11:5948111:C:A	F255L	0.877
11:5948111:C:G	F255L	0.877
11:5947650:T:C	F102L	0.868
11:5947652:C:A	F102L	0.868
11:5947652:C:G	F102L	0.868
11:5947968:T:A	W208R	0.862
11:5947968:T:C	W208R	0.862
11:5947393:T:G	F16C	0.846
11:5947407:T:C	F21L	0.841
11:5947409:T:A	F21L	0.841
11:5947409:T:G	F21L	0.841
11:5947712:G:A	M122I	0.838
11:5947712:G:C	M122I	0.838
11:5947712:G:T	M122I	0.838
11:5947901:T:A	N185K	0.832
11:5947901:T:G	N185K	0.832
11:5947723:G:C	R126P	0.813
11:5948215:C:A	A290D	0.812
11:5947399:T:C	L18S	0.811
11:5947578:T:C	C78R	0.808

dbSNP variants (sampled 300 via entrez): RS1000018208 (11:5955849 C>T), RS1000073963 (11:5995877 A>G), RS1000082787 (11:5943871 G>A,C,T), RS1000083235 (11:5978130 G>A), RS1000148854 (11:5949537 G>A,T), RS1000164353 (11:5956953 C>T), RS1000210749 (11:6012035 C>A,T), RS1000218106 (11:5995942 A>G), RS1000228741 (11:6008466 C>A,G), RS1000262122 (11:5950368 A>T), RS1000335845 (11:5961792 A>C,G), RS1000367823 (11:6002240 G>A), RS1000387102 (11:5942477 T>A), RS1000429358 (11:5962123 T>G), RS1000492752 (11:5996218 G>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Valproic Acid	decreases methylation	1

Clinical trials (associated diseases)

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