OR1L3

Summary

OR1L3 (olfactory receptor family 1 subfamily L member 3, HGNC:8215) is a protein-coding gene on chromosome 9q33.2, encoding Olfactory receptor 1L3 (Q8NH93). 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 26735 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 37 total
• MANE Select transcript: NM_001005234

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8215
Approved symbol	OR1L3
Name	olfactory receptor family 1 subfamily L member 3
Location	9q33.2
Locus type	gene with protein product
Status	Approved
Aliases	OR9-D
Ensembl gene	ENSG00000171481
Ensembl biotype	protein_coding
Entrez	26735

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000304820

RefSeq mRNA: 1 — MANE Select: NM_001005234 NM_001005234

CCDS: CCDS35128

Canonical transcript exons

ENST00000304820 — 1 exons

Exon	Start	End
ENSE00001137222	122675130	122676104

Expression profiles

Bgee: expression breadth tissue_specific, 1 present calls, max score 41.89.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
colonic epithelium	UBERON:0000397	41.89	gold quality
bone marrow cell	CL:0002092	40.77	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
endometrium	UBERON:0001295	35.32	gold quality
bone marrow	UBERON:0002371	34.10	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
tonsil	UBERON:0002372	31.07	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
prefrontal cortex	UBERON:0000451	30.26	gold quality
monocyte	CL:0000576	29.98	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
leukocyte	CL:0000738	29.77	gold quality
liver	UBERON:0002107	29.35	gold quality
corpus callosum	UBERON:0002336	29.04	gold quality
gall bladder	UBERON:0002110	28.88	silver quality
duodenum	UBERON:0002114	28.14	gold quality
anterior cingulate cortex	UBERON:0009835	27.95	silver quality
adrenal tissue	UBERON:0018303	27.94	gold quality
primary visual cortex	UBERON:0002436	27.74	gold quality
lymph node	UBERON:0000029	27.57	gold quality
blood	UBERON:0000178	26.52	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
right lung	UBERON:0002167	25.13	gold quality
uterine cervix	UBERON:0000002	24.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.14

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

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), 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), OR4K17 (ENSG00000176230)

Protein

Protein identifiers

Olfactory receptor 1L3 — Q8NH93 (reviewed: Q8NH93)

Alternative names: Olfactory receptor 9-D, Olfactory receptor OR9-28

All UniProt accessions (2): A0A126GVD1, Q8NH93

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_001005234* (*=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 3, chain 1, glycosylation site 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NH93-F1	88.87	0.64

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): 97–189

Glycosylation sites (1): 5

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

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

MSigDB gene sets: 17 (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, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, REACTOME_OLFACTORY_SIGNALING_PATHWAY, REACTOME_SENSORY_PERCEPTION, GOBP_DETECTION_OF_CHEMICAL_STIMULUS, GOMF_MOLECULAR_TRANSDUCER_ACTIVITY

GO Biological Process (5): signal transduction (GO:0007165), G protein-coupled receptor signaling pathway (GO:0007186), sensory perception of chemical stimulus (GO:0007606), sensory perception of smell (GO:0007608), detection of chemical stimulus involved in sensory perception of smell (GO:0050911)

GO Molecular Function (4): G protein-coupled receptor activity (GO:0004930), olfactory receptor activity (GO:0004984), protein binding (GO:0005515), 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
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	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
binding	1
molecular transducer activity	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

120 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR1L3	SPATA21	Q7Z572	571
OR1L3	ZNF280A	P59817	506
OR1L3	SLC22A31	A6NKX4	506
OR1L3	ZNF276	Q8N554	476
OR1L3	JADE3	Q92613	435
OR1L3	TRAPPC2L	Q9UL33	419
OR1L3	RTP1	P59025	406
OR1L3	CPNE7	Q9UBL6	400
OR1L3	ACSF3	Q4G176	370
OR1L3	MROH8	Q9H579	323
OR1L3	AMELX	Q99217	321
OR1L3	GALNS	P34059	314
OR1L3	USP29	Q9HBJ7	310
OR1L3	PSG9	Q00887	310
OR1L3	A0A096LNM5	A0A096LNM5	305

IntAct

4 interactions, top by confidence:

A	B	Type	Score
OTX2	OR1L3	psi-mi:“MI:0915”(physical association)	0.560
OR1L3	OTX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): OR1L3 (Two-hybrid), OR1L3 (Affinity Capture-MS), OR1L3 (Affinity Capture-MS)

ESM2 similar proteins: A6NDH6, A6NDL8, A6NF89, A6NHG9, A6NIJ9, A6NJZ3, A6NKK0, A6NM76, P0C617, P0DN80, P34983, P37067, P37069, Q60884, Q60886, Q7TR96, Q8N162, Q8NGE1, Q8NGE2, Q8NGF7, Q8NGG5, Q8NGI8, Q8NGL4, Q8NGQ3, Q8NGS5, Q8NGV6, Q8NGV7, Q8NH89, Q8NH90, Q8NH92, Q8NH93, Q8NHB8, Q8NHC7, Q8VEW2, Q8VEW6, Q8VEX6, Q8VF12, Q8VF13, Q8VFB9, Q8VFD1

Diamond homologs: A0A096LPK9, A0A0X1KG70, A6NHA9, A6NMZ5, O76099, O95013, P0C604, P0C623, P0C645, P0DN82, P58180, Q13606, Q15615, Q60878, Q60881, Q60888, Q60893, Q6IEV9, Q6IEY1, Q6IF82, Q6UXT6, Q7TQQ0, Q8IXE1, Q8N0Y3, Q8NGA1, Q8NGA8, Q8NGB2, Q8NGB4, Q8NGB6, Q8NGB8, Q8NGB9, Q8NGC2, Q8NGC3, Q8NGC4, Q8NGC6, Q8NGD0, Q8NGD1, Q8NGD2, Q8NGD3, Q8NGD4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	35
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

341 predictions. Top by Δscore:

Variant	Effect	Δscore
9:122675787:A:G	acceptor_gain	0.7600
9:122675606:T:G	acceptor_gain	0.7500
9:122675807:CAAGA:C	acceptor_gain	0.7500
9:122675806:TCAAG:T	acceptor_gain	0.7400
9:122675808:AAGAT:A	acceptor_gain	0.7100
9:122675666:T:TA	acceptor_gain	0.6900
9:122675809:AGA:A	acceptor_gain	0.6800
9:122675593:A:AG	acceptor_gain	0.6700
9:122675603:A:AG	acceptor_gain	0.6500
9:122675786:A:AG	acceptor_gain	0.6500
9:122675302:C:G	donor_gain	0.6400
9:122675302:C:CG	donor_gain	0.6300
9:122675683:T:A	acceptor_gain	0.6000
9:122675805:CTCAA:C	acceptor_gain	0.5900
9:122675786:A:AC	acceptor_gain	0.5800
9:122675911:A:AG	acceptor_gain	0.5800
9:122675912:G:GG	acceptor_gain	0.5800
9:122675997:A:AG	acceptor_gain	0.5800
9:122675998:G:GG	acceptor_gain	0.5800
9:122675664:T:TA	acceptor_gain	0.5700
9:122675897:C:G	donor_gain	0.5700
9:122675605:A:AG	acceptor_gain	0.5600
9:122675810:G:T	acceptor_gain	0.5600
9:122675135:A:T	donor_gain	0.5500
9:122675594:C:G	acceptor_gain	0.5500
9:122675714:T:TA	acceptor_gain	0.5400
9:122675890:G:GG	donor_gain	0.5300
9:122675912:GC:G	acceptor_gain	0.5300
9:122675319:A:G	acceptor_gain	0.5200
9:122675614:T:TA	acceptor_gain	0.5200

AlphaMissense

2128 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:122675163:T:C	F12L	0.865
9:122675165:T:A	F12L	0.865
9:122675165:T:G	F12L	0.865
9:122675211:T:C	F28L	0.831
9:122675213:T:A	F28L	0.831
9:122675213:T:G	F28L	0.831
9:122675631:T:C	F168L	0.822
9:122675633:T:A	F168L	0.822
9:122675633:T:G	F168L	0.822
9:122675220:T:C	F31L	0.813
9:122675222:T:A	F31L	0.813
9:122675222:T:G	F31L	0.813
9:122675374:T:A	L82H	0.745
9:122675658:T:C	F177L	0.741
9:122675660:T:A	F177L	0.741
9:122675660:T:G	F177L	0.741
9:122675362:T:A	V78D	0.688
9:122675371:T:G	M81R	0.686
9:122675175:G:A	G16R	0.684
9:122675175:G:C	G16R	0.684
9:122675371:T:A	M81K	0.682
9:122675880:T:C	F251L	0.679
9:122675882:T:A	F251L	0.679
9:122675882:T:G	F251L	0.679
9:122675365:C:A	P79Q	0.671
9:122675841:T:C	F238L	0.659
9:122675843:C:A	F238L	0.659
9:122675843:C:G	F238L	0.659
9:122675365:C:G	P79R	0.648
9:122675889:A:C	S254R	0.647

dbSNP variants (sampled 300 via entrez): RS1001941077 (9:122676040 T>A,C), RS1005002182 (9:122673911 C>T), RS1005083352 (9:122674146 G>A), RS1007079405 (9:122674811 C>G,T), RS1008189462 (9:122674926 A>G), RS1008857128 (9:122673631 C>T), RS1008943540 (9:122673199 C>T), RS1008946316 (9:122673881 G>T), RS1009518791 (9:122676096 G>C), RS1009549003 (9:122676412 G>T), RS1011258767 (9:122675130 A>G), RS1012318359 (9:122674184 C>T), RS1012906331 (9:122674129 G>C), RS1013740201 (9:122675482 T>C), RS1017402242 (9:122676568 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
arsenite	decreases methylation	1
CGP 52608	affects binding, increases reaction	1
Cadmium	decreases expression	1

Clinical trials (associated diseases)

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