OR52B4

Summary

OR52B4 (olfactory receptor family 52 subfamily B member 4, HGNC:15209) is a protein-coding gene on chromosome 11p15.4, encoding Olfactory receptor 52B4 (Q8NGK2). 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. This olfactory receptor gene is a segregating pseudogene, where some individuals have an allele that encodes a functional olfactory receptor, while other individuals have an allele encoding a protein that is predicted to be non-functional.

Source: NCBI Gene 143496 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 60 total
• MANE Select transcript: NM_001005161

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15209
Approved symbol	OR52B4
Name	olfactory receptor family 52 subfamily B member 4
Location	11p15.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000221996
Ensembl biotype	protein_coding
Entrez	143496

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000624801

RefSeq mRNA: 1 — MANE Select: NM_001005161 NM_001005161

Canonical transcript exons

ENST00000624801 — 1 exons

Exon	Start	End
ENSE00001568512	4367263	4368386

Expression profiles

Bgee: expression breadth not_expressed, 0 present calls, max score 38.25.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bone marrow cell	CL:0002092	38.25	gold quality
colonic epithelium	UBERON:0000397	37.20	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
skeletal muscle tissue	UBERON:0001134	34.94	gold quality
muscle tissue	UBERON:0002385	33.43	gold quality
bone marrow	UBERON:0002371	32.81	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
right uterine tube	UBERON:0001302	30.42	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.04	gold quality
lymph node	UBERON:0000029	28.96	gold quality
tonsil	UBERON:0002372	28.67	gold quality
monocyte	CL:0000576	28.42	gold quality
leukocyte	CL:0000738	28.34	gold quality
duodenum	UBERON:0002114	28.14	gold quality
myometrium	UBERON:0001296	27.98	gold quality
smooth muscle tissue	UBERON:0001135	27.97	gold quality
urinary bladder	UBERON:0001255	27.84	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	27.54	gold quality
placenta	UBERON:0001987	27.50	gold quality
islet of Langerhans	UBERON:0000006	27.35	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
muscle of leg	UBERON:0001383	25.48	gold quality
fallopian tube	UBERON:0003889	25.46	gold quality
calcaneal tendon	UBERON:0003701	25.27	gold quality
right lung	UBERON:0002167	25.07	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• The association of variant rs4910623 in OR52B4 gene with anti-VEGF treatment response in age-related macular degeneration. OR52B4 single nucleotide polynorphism rs4910623 allele frequency in age-related macular degeneration patients. (PMID:27892514)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Or52b4	ENSMUSG00000073979
rattus_norvegicus	Or52b4	ENSRNOG00000012071
rattus_norvegicus	Olr385	ENSRNOG00000068067

Paralogs (51): OR51E2 (ENSG00000167332), OR51B5 (ENSG00000167355), OR51I1 (ENSG00000167359), OR51Q1 (ENSG00000167360), OR52A5 (ENSG00000171944), OR52W1 (ENSG00000175485), OR51B6 (ENSG00000176239), OR51V1 (ENSG00000176742), OR52E2 (ENSG00000176787), OR51L1 (ENSG00000176798), OR51G2 (ENSG00000176893), OR51A7 (ENSG00000176895), OR51T1 (ENSG00000176900), OR51S1 (ENSG00000176922), OR51F2 (ENSG00000176925), OR51E1 (ENSG00000180785), OR56B4 (ENSG00000180919), OR52E4 (ENSG00000180974), OR52N2 (ENSG00000180988), OR52N1 (ENSG00000181001), OR52N5 (ENSG00000181009), OR56B2 (ENSG00000181017), OR56B1 (ENSG00000181023), OR52N4 (ENSG00000181074), OR52P1 (ENSG00000181109), OR52D1 (ENSG00000181609), OR52H1 (ENSG00000181616), OR52K2 (ENSG00000181963), OR52A1 (ENSG00000182070), OR51B4 (ENSG00000183251), OR52E8 (ENSG00000183269), OR52L1 (ENSG00000183313), OR51M1 (ENSG00000184698), OR52B6 (ENSG00000187747), OR51I2 (ENSG00000187918), OR52K1 (ENSG00000196778), OR51D1 (ENSG00000197428), OR51C1 (ENSG00000197674), OR52M1 (ENSG00000197790), OR52E6 (ENSG00000205409)

Protein

Protein identifiers

Olfactory receptor 52B4 — Q8NGK2 (reviewed: Q8NGK2)

Alternative names: Olfactory receptor OR11-3

All UniProt accessions (2): Q8NGK2, A0A126GW82

UniProt curated annotations — full annotation on UniProt →

Function. Odorant receptor.

Subcellular location. Cell membrane.

Polymorphism. A stop codon at position Ala-40 in the gene coding for this protein is responsible for functional diversity thus producing a pseudogene. The stop codon is more frequent in non-Africans than in African-Americans.

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

RefSeq proteins (1): NP_001005161* (*=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 (19 total): topological domain 8, transmembrane region 7, chain 1, glycosylation site 1, disulfide bond 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NGK2-F1	87.58	0.60

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): 99–191

Glycosylation sites (1): 5

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 17 (showing top): GOBP_COGNITION, 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, OSMAN_BLOOD_CHAD63_KH_AGE_18_50YO_HIGH_DOSE_SUBJECTS_24HR_UP, GOBP_DETECTION_OF_CHEMICAL_STIMULUS, GOMF_MOLECULAR_TRANSDUCER_ACTIVITY, KONDO_PROSTATE_CANCER_WITH_H3K27ME3

GO Biological Process (6): cognition (GO:0050890), signal transduction (GO:0007165), G protein-coupled receptor signaling pathway (GO:0007186), sensory perception of smell (GO:0007608), nervous system process (GO:0050877), 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)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
transmembrane signaling receptor activity	2
nervous system 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
system process	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

138 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR52B4	ARMS2	P0C7Q2	448
OR52B4	ATAD2B	Q9ULI0	369
OR52B4	YY1AP1	Q9H869	368
OR52B4	SLC2A7	Q6PXP3	358
OR52B4	FAM181B	A6NEQ2	324
OR52B4	NKD2	Q969F2	311
OR52B4	RAPGEF5	Q92565	308
OR52B4	CCDC40	Q4G0X9	308
OR52B4	CFH	P08603	290
OR52B4	VWA3A	A6NCI4	259
OR52B4	MMP20	O60882	251
OR52B4	VWA3B	Q502W6	248
OR52B4	GTF2A1L	Q9UNN4	246
OR52B4	ST3GAL4	Q11206	245
OR52B4	CCT3	P49368	241

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A3B3IT45, A6NGY5, O88628, P0C646, Q6IFG1, Q8NGF0, Q8NGF1, Q8NGF3, Q8NGH6, Q8NGH7, Q8NGH9, Q8NGI0, Q8NGI2, Q8NGJ2, Q8NGJ3, Q8NGJ4, Q8NGJ5, Q8NGJ6, Q8NGJ7, Q8NGJ9, Q8NGK1, Q8NGK2, Q8NGK3, Q8NGK4, Q8NGK5, Q8NGK6, Q8NH53, Q8NH55, Q8NH56, Q8NH57, Q8NH59, Q8NH60, Q8NH61, Q8NH63, Q8NH64, Q8TCB6, Q8VBV9, Q96RD2, Q96RD3, Q9H255

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

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	56
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

173 predictions. Top by Δscore:

Variant	Effect	Δscore
11:4367631:A:T	acceptor_gain	0.9500
11:4367607:A:C	acceptor_gain	0.9400
11:4367607:A:AC	acceptor_gain	0.9200
11:4367606:CA:C	acceptor_gain	0.9100
11:4367609:G:C	acceptor_gain	0.9100
11:4367636:A:C	acceptor_gain	0.9100
11:4367630:CAGCA:C	acceptor_gain	0.8900
11:4367620:CA:C	acceptor_gain	0.8800
11:4367609:G:GC	acceptor_gain	0.8400
11:4367634:A:C	acceptor_gain	0.8100
11:4367621:A:AC	acceptor_gain	0.7600
11:4367621:A:C	acceptor_gain	0.7300
11:4368185:A:C	acceptor_gain	0.7100
11:4367937:A:AC	donor_gain	0.6800
11:4367593:CAT:C	acceptor_gain	0.6600
11:4367595:TC:T	acceptor_loss	0.6600
11:4367596:C:CA	acceptor_loss	0.6600
11:4367725:A:C	donor_gain	0.6500
11:4367633:CATA:C	acceptor_gain	0.6400
11:4367617:CAGCA:C	acceptor_gain	0.6200
11:4367621:A:T	acceptor_gain	0.6200
11:4367591:AGCAT:A	acceptor_gain	0.6100
11:4367596:C:CC	acceptor_gain	0.6100
11:4367618:A:T	acceptor_gain	0.6000
11:4367634:A:AC	acceptor_gain	0.6000
11:4367636:A:AC	acceptor_gain	0.6000
11:4367834:A:C	donor_gain	0.5700
11:4368324:T:TA	donor_gain	0.5700
11:4367620:C:CT	acceptor_loss	0.5500
11:4367720:A:AC	donor_gain	0.5500

AlphaMissense

2090 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:4367786:G:C	F170L	0.825
11:4367786:G:T	F170L	0.825
11:4367788:A:G	F170L	0.825
11:4368254:G:C	F14L	0.803
11:4368254:G:T	F14L	0.803
11:4368256:A:G	F14L	0.803
11:4367756:A:C	F180L	0.684
11:4367756:A:T	F180L	0.684
11:4367758:A:G	F180L	0.684
11:4367537:A:C	F253L	0.661
11:4367537:A:T	F253L	0.661
11:4367539:A:G	F253L	0.661
11:4368029:G:C	F89L	0.634
11:4368029:G:T	F89L	0.634
11:4368031:A:G	F89L	0.634
11:4367966:G:C	F110L	0.630
11:4367966:G:T	F110L	0.630
11:4367968:A:G	F110L	0.630
11:4368035:G:C	F87L	0.621
11:4368035:G:T	F87L	0.621
11:4368037:A:G	F87L	0.621
11:4367984:G:C	F104L	0.617
11:4367984:G:T	F104L	0.617
11:4367986:A:G	F104L	0.617
11:4367498:A:C	F266L	0.616
11:4367498:A:T	F266L	0.616
11:4367500:A:G	F266L	0.616
11:4368197:G:C	F33L	0.589
11:4368197:G:T	F33L	0.589
11:4368199:A:G	F33L	0.589

dbSNP variants (sampled 300 via entrez): RS1000589350 (11:4369998 A>G), RS1001634195 (11:4368972 G>T), RS1001772136 (11:4370305 A>C), RS1002001219 (11:4368777 G>A,T), RS1002875383 (11:4369253 G>A), RS1003045240 (11:4370310 G>A), RS1004883552 (11:4368779 T>G), RS1007174932 (11:4367031 A>G), RS1008307454 (11:4370005 A>G), RS1009109102 (11:4368337 G>A,T), RS1009290037 (11:4369346 T>C), RS1009405376 (11:4368904 C>T), RS1009762071 (11:4367819 G>A), RS1012095415 (11:4367450 G>A), RS1013110731 (11:4370339 T>A)

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

4 associations (top):

Study	Trait	p-value
GCST010725_20	Malaria	4.000000e-69
GCST010725_33	Malaria	2.000000e-67
GCST010725_51	Malaria	1.000000e-55
GCST011741_39	LDL cholesterol levels in HIV infection	8.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004611	low density lipoprotein cholesterol measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
CGP 52608	affects binding, increases reaction	1
Benzo(a)pyrene	affects methylation	1
Cadmium	decreases expression, increases abundance	1
Sodium Selenite	decreases expression	1
Cadmium Chloride	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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