OR13C9

Summary

OR13C9 (olfactory receptor family 13 subfamily C member 9, HGNC:15104) is a protein-coding gene on chromosome 9q31.1, encoding Olfactory receptor 13C9 (Q8NGT0). 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 286362 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 33 total
• MANE Select transcript: NM_001001956

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15104
Approved symbol	OR13C9
Name	olfactory receptor family 13 subfamily C member 9
Location	9q31.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000136839
Ensembl biotype	protein_coding
Entrez	286362

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000259362

RefSeq mRNA: 1 — MANE Select: NM_001001956 NM_001001956

CCDS: CCDS35093

Canonical transcript exons

ENST00000259362 — 1 exons

Exon	Start	End
ENSE00001705431	104617248	104618204

Expression profiles

Bgee: expression breadth tissue_specific, 5 present calls, max score 90.78.

Top tissues by expression

116 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	90.78	gold quality
bone marrow cell	CL:0002092	42.04	gold quality
ventricular zone	UBERON:0003053	39.95	gold quality
granulocyte	CL:0000094	37.87	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
bone marrow	UBERON:0002371	34.75	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
leukocyte	CL:0000738	31.99	gold quality
monocyte	CL:0000576	31.77	gold quality
adenohypophysis	UBERON:0002196	31.69	silver quality
corpus callosum	UBERON:0002336	31.61	gold quality
pituitary gland	UBERON:0000007	31.04	silver quality
sural nerve	UBERON:0015488	30.93	gold quality
adrenal tissue	UBERON:0018303	30.90	silver quality
tonsil	UBERON:0002372	30.61	gold quality
liver	UBERON:0002107	30.50	gold quality
prefrontal cortex	UBERON:0000451	29.96	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
gall bladder	UBERON:0002110	29.04	silver quality
duodenum	UBERON:0002114	28.14	gold quality
urinary bladder	UBERON:0001255	28.04	gold quality
lymph node	UBERON:0000029	27.57	gold quality
calcaneal tendon	UBERON:0003701	27.52	gold quality
islet of Langerhans	UBERON:0000006	27.30	gold quality
uterine cervix	UBERON:0000002	27.13	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
blood	UBERON:0000178	26.34	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	25.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.81

Regulation

Is transcription factor: no

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
rattus_norvegicus	Or13c9	ENSRNOG00000080507

Paralogs (92): OR2B6 (ENSG00000124657), 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), OR2D3 (ENSG00000178358), OR13D1 (ENSG00000179055), OR10A7 (ENSG00000179919), OR2Z1 (ENSG00000181733), OR2V2 (ENSG00000182613), OR10G7 (ENSG00000182634), OR2T29 (ENSG00000182783), OR2T34 (ENSG00000183310), OR2T10 (ENSG00000184022)

Protein

Protein identifiers

Olfactory receptor 13C9 — Q8NGT0 (reviewed: Q8NGT0)

Alternative names: Olfactory receptor OR9-13

All UniProt accessions (1): Q8NGT0

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_001001956* (*=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-Q8NGT0-F1	82.33	0.44

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: 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, GOBP_SENSORY_PERCEPTION_OF_SMELL, GOBP_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY, GOBP_DETECTION_OF_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION, CCTNTMAGA_UNKNOWN, ZFHX3_TARGET_GENES, 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 (3): nucleoplasm (GO:0005654), 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
cellular anatomical structure	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
nuclear lumen	1
membrane	1
cell periphery	1

Protein interactions and networks

STRING

66 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OR13C9	NIPSNAP3A	Q9UFN0	567
OR13C9	FRMD5	Q7Z6J6	476
OR13C9	FBXO10	Q9UK96	418
OR13C9	TOMM5	Q8N4H5	370
OR13C9	ATP6V0C	P27449	366
OR13C9	VWDE	Q8N2E2	311
OR13C9	GALNTL6	Q49A17	245
OR13C9	PLA2G7	Q13093	237
OR13C9	ABCA1	O95477	224
OR13C9	HNRNPCL1	O60812	220
OR13C9	DGCR2	P98153	217
OR13C9	AFG1L	Q8WV93	197
OR13C9	NIPA1	Q7RTP0	161
OR13C9	ZNF804A	Q7Z570	160
OR13C9	MUC6	Q6W4X9	156

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A096LPK9, A0A0X1KG70, A6NCV1, O95221, P0C7N1, P0C7N5, Q60881, Q60888, Q6IEU7, Q8NGA8, Q8NGB6, Q8NGC6, Q8NGD0, Q8NGD1, Q8NGD2, Q8NGD4, Q8NGD5, Q8NGE8, Q8NGF8, Q8NGI4, Q8NGI6, Q8NGJ1, Q8NGM9, Q8NGP8, Q8NGP9, Q8NGS9, Q8NGT0, Q8NH01, Q8NH10, Q8NH18, Q8NH21, Q8NH41, Q8NH42, Q8NH43, Q8NH49, Q8NH69, Q8NH85, Q8VEW5, Q8VF65, Q8VFD3

Diamond homologs: A3KFT3, A4D2G3, O43749, O60412, O76000, O76001, O76002, O95006, O95047, O95371, O95918, P0C626, P23266, P23269, P23272, P23273, P23274, P23275, P30953, P30955, P34982, P34984, P34986, P58173, P58181, P59922, P70526, Q13606, Q13607, Q15617, Q15619, Q5TZ20, Q60879, Q60890, Q6IEU7, Q6IF42, Q6UXT6, Q8N628, Q8NGA1, Q8NGC9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

279 predictions. Top by Δscore:

Variant	Effect	Δscore
9:104618136:AAG:A	donor_gain	0.8100
9:104617620:ATTG:A	donor_gain	0.7800
9:104617530:GATG:G	acceptor_gain	0.7700
9:104618136:AAGC:A	donor_gain	0.7400
9:104617529:GGATG:G	acceptor_gain	0.7100
9:104617531:A:C	acceptor_gain	0.6900
9:104618158:C:A	donor_gain	0.6900
9:104617534:C:CC	acceptor_gain	0.6600
9:104617623:G:A	donor_gain	0.6500
9:104618132:A:C	donor_gain	0.6500
9:104618136:A:AC	donor_gain	0.6500
9:104617532:TG:T	acceptor_gain	0.6400
9:104618137:A:C	donor_gain	0.6400
9:104617350:CCCA:C	acceptor_gain	0.6300
9:104617531:ATG:A	acceptor_gain	0.6300
9:104617620:ATTGC:A	donor_gain	0.6300
9:104617532:TGCT:T	acceptor_loss	0.6200
9:104617533:GCT:G	acceptor_loss	0.6200
9:104617534:C:CA	acceptor_loss	0.6200
9:104618016:C:T	acceptor_gain	0.6200
9:104617315:C:CC	acceptor_gain	0.6000
9:104617544:T:TC	acceptor_gain	0.5900
9:104617459:A:AC	donor_gain	0.5700
9:104617957:A:AC	donor_gain	0.5700
9:104617958:C:CC	donor_gain	0.5700
9:104618016:C:CT	acceptor_gain	0.5700
9:104617352:CA:C	acceptor_gain	0.5600
9:104618138:G:A	donor_gain	0.5600
9:104617507:C:A	donor_gain	0.5500
9:104617531:ATGCT:A	acceptor_gain	0.5400

AlphaMissense

2119 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:104617314:A:C	S297R	0.973
9:104617314:A:T	S297R	0.973
9:104617316:T:G	S297R	0.973
9:104617471:A:G	L245P	0.970
9:104617840:C:G	R122P	0.970
9:104617452:G:C	F251L	0.969
9:104617452:G:T	F251L	0.969
9:104617454:A:G	F251L	0.969
9:104617851:C:A	M118I	0.963
9:104617851:C:G	M118I	0.963
9:104617851:C:T	M118I	0.963
9:104617497:T:A	K236N	0.962
9:104617497:T:G	K236N	0.962
9:104617329:A:C	N292K	0.958
9:104617329:A:T	N292K	0.958
9:104617828:A:T	I126N	0.956
9:104617843:T:G	D121A	0.954
9:104617308:T:A	R299S	0.951
9:104617308:T:G	R299S	0.951
9:104617843:T:A	D121V	0.949
9:104617828:A:C	I126S	0.943
9:104617832:C:G	A125P	0.942
9:104617842:G:C	D121E	0.942
9:104617842:G:T	D121E	0.942
9:104617760:A:G	W149R	0.940
9:104617760:A:T	W149R	0.940
9:104617459:A:T	I249K	0.939
9:104617841:G:T	R122S	0.938
9:104617576:G:C	P210R	0.934
9:104617491:G:C	F238L	0.930

dbSNP variants (sampled 300 via entrez): RS1001357547 (9:104619098 T>C), RS1002411743 (9:104619860 T>C), RS1003418111 (9:104618418 T>C), RS1004794282 (9:104620096 T>A,G), RS1006925872 (9:104619019 C>G), RS1007839900 (9:104619446 TAAG>T), RS1009216772 (9:104619903 T>C), RS1010543820 (9:104619401 T>G), RS1010684262 (9:104618441 G>A), RS1014094401 (9:104620144 C>G,T), RS1016002555 (9:104616768 G>A), RS1017222755 (9:104619141 C>T), RS1017441129 (9:104619959 C>T), RS1018864429 (9:104618481 A>G), RS1020181228 (9:104619430 A>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

1 associations (top):

Study	Trait	p-value
GCST009312_1	Antisaccade task score	3.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007969	cognitive inhibition 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
Cadmium	decreases expression, increases abundance	1
Endosulfan	decreases expression	1
Valproic Acid	decreases methylation	1
Cadmium Chloride	increases abundance, decreases expression	1

Clinical trials (associated diseases)

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