OBP2A

Summary

OBP2A (odorant binding protein 2A, HGNC:23380) is a protein-coding gene on chromosome 9q34.3, encoding Odorant-binding protein 2a (Q9NY56). Binds and transports small hydrophobic volatile molecules with a higher affinity for aldehydes and large fatty acids, including undecanal, palmitic acid, efficient aldehydes, benzenic aldehydes, heterocyclic aldehydes and aliphatic acids.

This gene encodes a small extracellular protein belonging to the lipocalin superfamily. The protein is thought to transport small, hydrophobic, volatile molecules or odorants through the nasal mucus to olfactory receptors, and may also function as a scavenger of highly concentrated or toxic odors. The protein is expressed as a monomer in the nasal mucus, and can bind diverse types of odorants with a higher affinity for aldehydes and fatty acids. This gene and a highly similar family member are located in a cluster of lipocalin genes on chromosome 9. Alternatively spliced transcript variants have been described, but their biological validity has not been determined.

Source: NCBI Gene 29991 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 59 total
• MANE Select transcript: NM_014582

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23380
Approved symbol	OBP2A
Name	odorant binding protein 2A
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Aliases	hOBPIIa, OBP, LCN13
Ensembl gene	ENSG00000122136
Ensembl biotype	protein_coding
OMIM	164320
Entrez	29991

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 nonsense_mediated_decay

ENST00000340780, ENST00000342114, ENST00000371776, ENST00000471886, ENST00000537747, ENST00000539850, ENST00000619164, ENST00000955692

RefSeq mRNA: 4 — MANE Select: NM_014582 NM_001293189, NM_001293193, NM_001412135, NM_014582

CCDS: CCDS6992, CCDS78455, CCDS78456

Canonical transcript exons

ENST00000371776 — 7 exons

Exon	Start	End
ENSE00001772644	135549837	135549969
ENSE00002341181	135546778	135546911
ENSE00003512457	135549308	135549331
ENSE00003560722	135548708	135548809
ENSE00003607084	135547871	135547981
ENSE00003681510	135547178	135547248
ENSE00003907292	135546126	135546252

Expression profiles

Bgee: expression breadth broad, 91 present calls, max score 80.14.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0087 / max 6.3152, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
205664	0.0087	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right uterine tube	UBERON:0001302	80.14	gold quality
vena cava	UBERON:0004087	78.10	gold quality
subthalamic nucleus	UBERON:0001906	75.52	gold quality
body of tongue	UBERON:0011876	74.49	gold quality
cardia of stomach	UBERON:0001162	74.34	gold quality
substantia nigra pars reticulata	UBERON:0001966	74.31	gold quality
tongue	UBERON:0001723	74.02	gold quality
dorsal plus ventral thalamus	UBERON:0001897	73.92	gold quality
thymus	UBERON:0002370	73.85	gold quality
cerebellar vermis	UBERON:0004720	73.71	gold quality
inferior vagus X ganglion	UBERON:0005363	73.64	gold quality
superior surface of tongue	UBERON:0007371	73.56	gold quality
pharyngeal mucosa	UBERON:0000355	73.49	gold quality
saphenous vein	UBERON:0007318	73.49	gold quality
lateral globus pallidus	UBERON:0002476	73.46	gold quality
pericardium	UBERON:0002407	73.40	gold quality
nipple	UBERON:0002030	73.34	gold quality
ventral tegmental area	UBERON:0002691	73.30	gold quality
substantia nigra pars compacta	UBERON:0001965	73.24	gold quality
lateral nuclear group of thalamus	UBERON:0002736	73.13	gold quality
pylorus	UBERON:0001166	73.05	gold quality
pons	UBERON:0000988	73.04	gold quality
trachea	UBERON:0003126	72.71	gold quality
trigeminal ganglion	UBERON:0001675	72.67	gold quality
medulla oblongata	UBERON:0001896	72.49	gold quality
renal medulla	UBERON:0000362	72.44	gold quality
dorsal root ganglion	UBERON:0000044	72.41	gold quality
synovial joint	UBERON:0002217	72.40	gold quality
layer of synovial tissue	UBERON:0007616	72.30	gold quality
superior vestibular nucleus	UBERON:0007227	72.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.66

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

6 targeting OBP2A, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-6510-5P	99.14	66.59	1081
HSA-MIR-760	98.81	66.65	1392
HSA-MIR-4456	97.50	64.88	1678
HSA-MIR-5702	96.68	68.21	958

Literature-anchored findings (GeneRIF, showing 12)

• hOBPIIa(alpha) is expressed in the nasal mucus covering the olfactory cleft and is able to bind numerous odorants of diverse chemical structures, with a higher affinity for aldehydes and large fatty acids. (PMID:12044155)
• Lys112 is the major determinant for governing hOBP-2A specificity towards aldehydes and small carboxylic acids. (PMID:16546182)
• Studied the crystallographic structure of human odorant-binding protein, OBPIIa at 2.6 A resolution. (PMID:25810031)
• This study demonstrated that the OBPIIa is associated with bitter sensitivity in human. (PMID:28487220)
• Importantly, OBPIIa gene polymorphism showed an effect on Parkinson’s disease-related olfactory deficits only in women. (PMID:30944919)
• Association between the rs2590498 polymorphism of Odorant Binding Protein (OBPIIa) gene and olfactory performance in healthy subjects. (PMID:31195037)
• Effect of the rs2890498 polymorphism of the OBPIIa gene on the human ability to smell single molecules. (PMID:33422593)
• Changes of Taste, Smell and Eating Behavior in Patients Undergoing Bariatric Surgery: Associations with PROP Phenotypes and Polymorphisms in the Odorant-Binding Protein OBPIIa and CD36 Receptor Genes. (PMID:33467165)
• Olfactory Function in Patients with Inflammatory Bowel Disease (IBD) Is Associated with Their Body Mass Index and Polymorphism in the Odor Binding-Protein (OBPIIa) Gene. (PMID:33671721)
• A polymorphism in the human gene encoding OBPIIa affects the perceived intensity of smelled odors. (PMID:35341882)
• Tumor-derived OBP2A promotes prostate cancer castration resistance. (PMID:36547668)
• Elevated expression of LCN13 through FXR activation ameliorates hepatocellular lipid accumulation and inflammation. (PMID:38493698)

Cross-species orthologs

9 orthologs

Organism	Symbol	Gene ID
mus_musculus	Lcn4	ENSMUSG00000026919
mus_musculus	Obp2a	ENSMUSG00000062061
mus_musculus	Obp2b	ENSMUSG00000079539
rattus_norvegicus	Lcn4	ENSRNOG00000030708
rattus_norvegicus	Obp2a	ENSRNOG00000042407
rattus_norvegicus	Lcn4l2	ENSRNOG00000043494
rattus_norvegicus	AABR07051244.1	ENSRNOG00000047422
rattus_norvegicus	Obp2b	ENSRNOG00000048417
rattus_norvegicus	Obp2bl1	ENSRNOG00000064942

Paralogs (12): PTGDS (ENSG00000107317), PAEP (ENSG00000122133), LCN2 (ENSG00000148346), LCN9 (ENSG00000148386), LCN1 (ENSG00000160349), OBP2B (ENSG00000171102), LCN15 (ENSG00000177984), LCN12 (ENSG00000184925), LCN10 (ENSG00000187922), LCN8 (ENSG00000204001), LCNL1 (ENSG00000214402), LCN6 (ENSG00000267206)

Protein

Protein identifiers

Odorant-binding protein 2a — Q9NY56 (reviewed: Q9NY56)

Alternative names: Odorant-binding protein IIa

All UniProt accessions (6): A0A087WXL2, Q9NY56, F2Z2D7, F5H159, Q5T8A4, Q5T8A5

UniProt curated annotations — full annotation on UniProt →

Function. Binds and transports small hydrophobic volatile molecules with a higher affinity for aldehydes and large fatty acids, including undecanal, palmitic acid, efficient aldehydes, benzenic aldehydes, heterocyclic aldehydes and aliphatic acids.

Subunit / interactions. Monomer.

Subcellular location. Secreted.

Tissue specificity. Strongly expressed in the nasal structures, salivary and lachrymal glands, and lung. Expressed in the liver.

Similarity. Belongs to the calycin superfamily. Lipocalin family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9NY56-1	Aa	yes
Q9NY56-2	Ab
Q9NY56-3	Ad
Q9NY56-4	Ag

RefSeq proteins (4): NP_001280118, NP_001280122, NP_001399064, NP_055397* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000566	Lipocln_cytosolic_FA-bd_dom	Domain
IPR002345	Lipocalin	Family
IPR002450	von_Ebner_gland	Family
IPR012674	Calycin	Homologous_superfamily

Pfam: PF00061

UniProt features (28 total): strand 9, sequence variant 4, mutagenesis site 3, helix 3, splice variant 3, sequence conflict 2, signal peptide 1, chain 1, disulfide bond 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4RUN	X-RAY DIFFRACTION	2.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NY56-F1	89.13	0.74

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): 74–166

Mutagenesis-validated functional residues (3):

Position	Phenotype
77	no effect on binding affinity for undecanal, palmitic acid, efficient aldehydes, benzenic aldehydes, heterocyclic aldehy
97	no effect on binding affinity for undecanal, palmitic acid, efficient aldehydes, benzenic aldehydes, heterocyclic aldehy
127	decreases binding affinity for undecanal, efficient aldehydes and aliphatic acids from 9- to 12-carbons long. no effect

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 27 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, GOBP_CARBOHYDRATE_HOMEOSTASIS, GOBP_SENSORY_PERCEPTION, KIM_GASTRIC_CANCER_CHEMOSENSITIVITY, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOBP_HOMEOSTATIC_PROCESS, GOBP_CHEMICAL_HOMEOSTASIS, GOMF_ODORANT_BINDING, GOBP_SENSORY_PERCEPTION_OF_SMELL, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN, chr9q34, GSE10325_BCELL_VS_LUPUS_BCELL_UP, MIR4456

GO Biological Process (3): sensory perception of chemical stimulus (GO:0007606), sensory perception of smell (GO:0007608), glucose homeostasis (GO:0042593)

GO Molecular Function (2): odorant binding (GO:0005549), small molecule binding (GO:0036094)

GO Cellular Component (2): obsolete extracellular space (GO:0005615), extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
sensory perception	1
sensory perception of chemical stimulus	1
carbohydrate homeostasis	1
cellular anatomical structure	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

5 interactions, top by confidence:

A	B	Type	Score
OBP2A	PPIB	psi-mi:“MI:0915”(physical association)	0.400
OBP2A	ADRB2	psi-mi:“MI:0915”(physical association)	0.370
OBP2A	CLN5	psi-mi:“MI:0914”(association)	0.350
OBP2A	TXNDC15	psi-mi:“MI:0914”(association)	0.350

BioGRID (16): OBP2B (Affinity Capture-MS), LRP2 (Affinity Capture-MS), CLN5 (Affinity Capture-MS), MOXD1 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), TXNDC15 (Affinity Capture-MS), OBP2B (Affinity Capture-MS), ERBB2IP (Affinity Capture-MS), TXNDC15 (Affinity Capture-MS), COL6A2 (Affinity Capture-MS), CLN5 (Affinity Capture-MS), OBP2A (Proximity Label-MS), OBP2A (Two-hybrid), TXNDC15 (Affinity Capture-MS), ERBB2IP (Affinity Capture-MS)

ESM2 similar proteins: B3EY83, B5X0G2, H2B3G5, O02853, O09114, O18873, O97921, P02758, P02761, P04119, P07380, P09466, P11588, P11672, P13613, P19647, P20289, P22057, P30152, P31025, P33685, P33686, P33687, P33688, P41222, P41244, P53715, P62502, P62503, P80188, Q28388, Q29095, Q29487, Q29562, Q5VSP4, Q6JVE6, Q6JVL5, Q6UWW0, Q810Z1, Q8K1H9

Diamond homologs: O18873, P20289, P20462, P31025, P41244, P53715, Q29144, Q5VSP4, Q62471, Q62472, Q8K1H9, Q8SQ30, Q9NPH6, Q9NY56, P02755, P02756, Q8WX39, P07380

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	44
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1258 predictions. Top by Δscore:

Variant	Effect	Δscore
9:135546247:G:GT	donor_gain	1.0000
9:135546258:C:G	donor_gain	1.0000
9:135546912:G:GG	donor_gain	1.0000
9:135546912:GTGA:G	donor_loss	1.0000
9:135546913:T:TC	donor_loss	1.0000
9:135546914:G:GG	donor_loss	1.0000
9:135547177:GGA:G	acceptor_gain	1.0000
9:135547245:GCCT:G	donor_gain	1.0000
9:135547249:G:GG	donor_gain	1.0000
9:135547869:A:AG	acceptor_gain	1.0000
9:135547869:AGATG:A	acceptor_gain	1.0000
9:135547870:G:GG	acceptor_gain	1.0000
9:135547870:GAT:G	acceptor_gain	1.0000
9:135547870:GATGG:G	acceptor_gain	1.0000
9:135547970:G:GT	donor_gain	1.0000
9:135547970:G:T	donor_gain	1.0000
9:135547971:A:T	donor_gain	1.0000
9:135547974:GCTT:G	donor_gain	1.0000
9:135548080:G:GT	donor_gain	1.0000
9:135548805:GACGG:G	donor_gain	1.0000
9:135548808:GG:G	donor_gain	1.0000
9:135548809:GG:G	donor_gain	1.0000
9:135548815:G:GT	donor_gain	1.0000
9:135548824:GCCC:G	donor_gain	1.0000
9:135546244:G:GT	donor_gain	0.9900
9:135546250:GAT:G	donor_gain	0.9900
9:135546253:G:GG	donor_gain	0.9900
9:135546777:G:GT	acceptor_loss	0.9900
9:135546777:GATC:G	acceptor_gain	0.9900
9:135546777:GATCA:G	acceptor_gain	0.9900

AlphaMissense

1112 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:135547239:T:C	F90L	0.948
9:135547241:C:A	F90L	0.948
9:135547241:C:G	F90L	0.948
9:135548746:T:C	F143L	0.935
9:135548748:T:A	F143L	0.935
9:135548748:T:G	F143L	0.935
9:135546901:T:C	F66L	0.911
9:135546903:C:A	F66L	0.911
9:135546903:C:G	F66L	0.911
9:135546895:G:C	A64P	0.904
9:135546907:T:C	F68L	0.876
9:135546909:C:A	F68L	0.876
9:135546909:C:G	F68L	0.876
9:135547213:T:C	M81T	0.846
9:135547240:T:C	F90S	0.844
9:135546792:G:C	W29C	0.832
9:135546792:G:T	W29C	0.832
9:135546802:G:C	A33P	0.830
9:135548747:T:C	F143S	0.815
9:135547927:T:C	F112L	0.814
9:135547929:T:A	F112L	0.814
9:135547929:T:G	F112L	0.814
9:135548791:T:C	F158L	0.812
9:135548793:C:A	F158L	0.812
9:135548793:C:G	F158L	0.812
9:135546790:T:A	W29R	0.811
9:135546790:T:C	W29R	0.811
9:135547191:T:A	C74S	0.804
9:135547192:G:C	C74S	0.804
9:135547240:T:G	F90C	0.774

dbSNP variants (sampled 300 via entrez): RS1001032053 (9:135550236 G>A), RS1001338849 (9:135545920 G>A,T), RS1001441799 (9:135550118 G>C), RS1002618305 (9:135549831 G>A), RS1003789746 (9:135544777 A>G), RS1005026429 (9:135548556 T>C), RS1007030129 (9:135550380 T>C), RS1007433304 (9:135546206 C>T), RS1007745433 (9:135547300 G>A,C), RS1008027453 (9:135545380 T>C), RS1008031379 (9:135549595 C>G,T), RS1009204120 (9:135545131 C>A,T), RS1009349105 (9:135548879 C>G,T), RS1010194451 (9:135546098 T>C), RS1010856614 (9:135544148 A>T)

Disease associations

OMIM: gene MIM:164320 | 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
GCST001793_1	Coagulation factor levels	4.000000e-34
GCST001793_4	Coagulation factor levels	1.000000e-128
GCST005091_4	Subcutaneous adipose tissue	1.000000e-06
GCST005092_1	Subcutaneous adipose tissue (sex interaction)	1.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008343	sex interaction measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol F	affects cotreatment, increases methylation	1
terbufos	increases methylation	1
1-anilino-8-naphthalenesulfonate	affects binding	1
11-(dansylamino)undecanoic acid	affects binding	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Benzo(a)pyrene	decreases methylation	1
Catechin	affects cotreatment, decreases expression	1
Fonofos	increases methylation	1
Nickel	decreases expression	1
Parathion	increases methylation	1
Plant Extracts	affects cotreatment, decreases expression	1
Tretinoin	affects binding	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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