OR2D3

Summary

OR2D3 (olfactory receptor family 2 subfamily D member 3, HGNC:15146) is a protein-coding gene on chromosome 11p15.4, encoding Olfactory receptor 2D3 (Q8NGH3). 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 120775 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 50 total
• MANE Select transcript: NM_001004684

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15146
Approved symbol	OR2D3
Name	olfactory receptor family 2 subfamily D member 3
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000178358
Ensembl biotype	protein_coding
Entrez	120775

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000317834

RefSeq mRNA: 1 — MANE Select: NM_001004684 NM_001004684

CCDS: CCDS31417

Canonical transcript exons

ENST00000317834 — 1 exons

Exon	Start	End
ENSE00000000003	6921002	6921994

Expression profiles

Bgee: expression breadth tissue_specific, 6 present calls, max score 93.03.

Top tissues by expression

128 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	93.03	gold quality
bone marrow cell	CL:0002092	56.20	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	52.86	gold quality
colonic epithelium	UBERON:0000397	42.01	gold quality
corpus callosum	UBERON:0002336	41.54	silver quality
sural nerve	UBERON:0015488	38.64	gold quality
granulocyte	CL:0000094	37.21	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
calcaneal tendon	UBERON:0003701	35.69	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
right uterine tube	UBERON:0001302	34.87	gold quality
tonsil	UBERON:0002372	34.70	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
primary visual cortex	UBERON:0002436	32.25	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
urinary bladder	UBERON:0001255	31.16	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
prefrontal cortex	UBERON:0000451	29.94	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
liver	UBERON:0002107	29.45	gold quality
lymph node	UBERON:0000029	28.93	gold quality
leukocyte	CL:0000738	28.21	gold quality
duodenum	UBERON:0002114	28.14	gold quality
adrenal tissue	UBERON:0018303	27.76	gold quality
monocyte	CL:0000576	27.63	gold quality
right coronary artery	UBERON:0001625	27.57	gold quality
superior frontal gyrus	UBERON:0002661	27.09	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality
blood	UBERON:0000178	26.51	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.63

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Or2d36	ENSMUSG00000073896
rattus_norvegicus	Or2d36b	ENSRNOG00000073684
rattus_norvegicus	Or2d36	ENSRNOG00000087705

Paralogs (92): OR2B6 (ENSG00000124657), OR13C9 (ENSG00000136839), OR13C4 (ENSG00000148136), OR2M5 (ENSG00000162727), OR10A5 (ENSG00000166363), OR2D2 (ENSG00000166368), OR2B2 (ENSG00000168131), OR2C1 (ENSG00000168158), OR13J1 (ENSG00000168828), OR10G3 (ENSG00000169208), OR10A3 (ENSG00000170683), OR10A4 (ENSG00000170782), OR10A2 (ENSG00000170790), OR13H1 (ENSG00000171054), OR2K2 (ENSG00000171133), OR2M4 (ENSG00000171180), OR10H2 (ENSG00000171942), OR10H5 (ENSG00000172519), OR10AD1 (ENSG00000172640), OR2Y1 (ENSG00000174339), OR10AG1 (ENSG00000174970), OR2T1 (ENSG00000175143), OR10P1 (ENSG00000175398), OR2T35 (ENSG00000177151), OR2M7 (ENSG00000177186), OR2T12 (ENSG00000177201), OR2T33 (ENSG00000177212), OR2AJ1 (ENSG00000177275), OR2T8 (ENSG00000177462), OR2G3 (ENSG00000177476), OR2G2 (ENSG00000177489), OR2B11 (ENSG00000177535), OR13D1 (ENSG00000179055), OR10A7 (ENSG00000179919), OR2Z1 (ENSG00000181733), OR2V2 (ENSG00000182613), OR10G7 (ENSG00000182634), OR2T29 (ENSG00000182783), OR2T34 (ENSG00000183310), OR2T10 (ENSG00000184022)

Protein

Protein identifiers

Olfactory receptor 2D3 — Q8NGH3 (reviewed: Q8NGH3)

Alternative names: Olfactory receptor OR11-89

All UniProt accessions (1): Q8NGH3

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_001004684* (*=MANE)

Domains & families (InterPro)

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

Pfam: PF13853

UniProt features (20 total): topological domain 8, transmembrane region 7, sequence variant 3, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NGH3-F1	87.03	0.67

Functional residue map

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

Glycosylation sites (1): 21

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_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, BRUINS_UVC_RESPONSE_LATE, GOBP_SENSORY_PERCEPTION_OF_SMELL, GOBP_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY, GOBP_DETECTION_OF_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION, ZWANG_DOWN_BY_2ND_EGF_PULSE, REACTOME_OLFACTORY_SIGNALING_PATHWAY, REACTOME_SENSORY_PERCEPTION, GOBP_DETECTION_OF_CHEMICAL_STIMULUS

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

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-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
sensory perception of smell	1
detection of chemical stimulus involved in sensory perception	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
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

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR2D3	ZNF215	Q9UL58	501
OR2D3	ZNF880	Q6PDB4	471
OR2D3	ZNF433	Q8N7K0	432
OR2D3	AFAP1L1	Q8TED9	431
OR2D3	ZNF214	Q9UL59	421
OR2D3	OAZ2	O95190	418
OR2D3	NUDT19	A8MXV4	379
OR2D3	GIMAP8	Q8ND71	354
OR2D3	CACNG7	P62955	341
OR2D3	POLN	Q7Z5Q5	316
OR2D3	GIMAP7	Q8NHV1	314
OR2D3	ATP8A1	Q9Y2Q0	314
OR2D3	NLRP14	Q86W24	305
OR2D3	ADAMTSL1	Q8N6G6	301
OR2D3	ARPC1A	Q92747	296

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A6NCV1, A6NF89, A6NJZ3, A6NL08, A6NM76, O76000, O95007, O95221, P0C626, P0C629, P30955, P37070, P70526, Q15617, Q15620, Q60882, Q60893, Q60895, Q6IEU7, Q8N0Y5, Q8N162, Q8NGE1, Q8NGG4, Q8NGG8, Q8NGH3, Q8NGL1, Q8NGP8, Q8NGP9, Q8NGR5, Q8NGR8, Q8NGS4, Q8NGT1, Q8NGX3, Q8NH01, Q8VEW5, Q8VF66, Q8VF76, Q8VFD0, Q8VFD3, Q8VFK2

Diamond homologs: A0A2R8YED5, O14581, O43749, O76099, O95221, P0C626, P0C7N1, P0C7N5, P0DN81, P23266, P23275, P30955, P47890, P58173, P58181, P59922, Q15617, Q15619, Q15622, Q60878, Q60881, Q60895, Q6IEU7, Q6UXT6, Q7TQQ0, Q7Z3T1, Q8N0Y5, Q8N146, Q8N162, Q8N628, Q8NG98, Q8NGA1, Q8NGC2, Q8NGE5, Q8NGF4, Q8NGF8, Q8NGG0, Q8NGG3, Q8NGG4, Q8NGG8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

247 predictions. Top by Δscore:

Variant	Effect	Δscore
11:6921804:ATG:A	acceptor_gain	0.7700
11:6921806:G:A	acceptor_gain	0.7500
11:6921366:T:TA	acceptor_gain	0.7100
11:6921077:TCC:T	donor_gain	0.6100
11:6921747:G:GT	donor_gain	0.5900
11:6921721:T:A	acceptor_gain	0.5700
11:6921743:G:GT	donor_gain	0.5600
11:6921700:T:G	donor_gain	0.5300
11:6921694:T:A	acceptor_gain	0.5200
11:6921805:T:G	acceptor_gain	0.5200
11:6921861:A:G	donor_gain	0.5200
11:6921039:C:T	donor_gain	0.5000
11:6921075:TGTCC:T	donor_gain	0.5000
11:6921107:G:GT	donor_gain	0.5000
11:6921371:G:A	acceptor_gain	0.5000
11:6921805:T:TA	acceptor_gain	0.4900
11:6921860:GA:G	donor_gain	0.4900
11:6921225:T:G	donor_gain	0.4700
11:6921290:GT:G	donor_gain	0.4700
11:6921335:G:A	acceptor_gain	0.4700
11:6921203:G:GT	donor_gain	0.4600
11:6921128:C:G	donor_gain	0.4400
11:6921370:T:A	acceptor_gain	0.4400
11:6921656:G:GT	donor_gain	0.4400
11:6921804:AT:A	acceptor_gain	0.4400
11:6921806:GGGT:G	acceptor_gain	0.4400
11:6921813:G:GT	donor_gain	0.4400
11:6921226:G:GG	donor_gain	0.4300
11:6921661:G:GA	donor_gain	0.4300
11:6921665:A:AG	donor_gain	0.4300

AlphaMissense

2163 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:6921083:T:C	F28L	0.871
11:6921085:T:A	F28L	0.871
11:6921085:T:G	F28L	0.871
11:6921800:T:C	F267L	0.865
11:6921802:C:A	F267L	0.865
11:6921802:C:G	F267L	0.865
11:6921403:G:A	M134I	0.787
11:6921403:G:C	M134I	0.787
11:6921403:G:T	M134I	0.787
11:6921920:A:C	S307R	0.786
11:6921922:C:A	S307R	0.786
11:6921922:C:G	S307R	0.786
11:6921414:G:C	R138P	0.782
11:6921907:C:A	N302K	0.770
11:6921907:C:G	N302K	0.770
11:6921581:T:C	F194L	0.766
11:6921583:T:A	F194L	0.766
11:6921583:T:G	F194L	0.766
11:6921757:G:C	K252N	0.753
11:6921757:G:T	K252N	0.753
11:6921761:T:C	F254L	0.753
11:6921763:T:A	F254L	0.753
11:6921763:T:G	F254L	0.753
11:6921233:T:C	F78L	0.744
11:6921235:T:A	F78L	0.744
11:6921235:T:G	F78L	0.744
11:6921412:C:A	D137E	0.739
11:6921412:C:G	D137E	0.739
11:6921230:T:C	F77L	0.715
11:6921232:T:A	F77L	0.715

dbSNP variants (sampled 300 via entrez): RS1001026029 (11:6919389 C>T), RS1001547847 (11:6922364 C>T), RS1001579078 (11:6922020 T>A,C,G), RS1003162946 (11:6919451 T>C), RS1005033125 (11:6922421 C>G), RS1008379408 (11:6919907 A>T), RS1012140035 (11:6920546 A>G), RS1012187248 (11:6919521 T>C), RS1012980278 (11:6920776 G>A), RS1013158024 (11:6921068 A>C), RS1013953298 (11:6922285 C>A), RS1015174507 (11:6919836 C>G), RS1015460620 (11:6919512 G>A), RS1015543208 (11:6922430 T>C), RS1016987756 (11:6919351 T>C)

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

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, affects cotreatment	1
Fulvestrant	affects cotreatment, decreases methylation	1
Atrazine	increases expression	1
Benzo(a)pyrene	increases methylation	1
Endosulfan	increases expression	1
Phthalic Acids	decreases expression	1
Tretinoin	increases expression	1

Clinical trials (associated diseases)

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