RTP3

Summary

RTP3 (receptor transporter protein 3, HGNC:15572) is a protein-coding gene on chromosome 3p21.31, encoding Receptor-transporting protein 3 (Q9BQQ7). Promotes functional cell surface expression of the bitter taste receptors TAS2R16 and TAS2R43.

Predicted to enable olfactory receptor binding activity. Involved in detection of chemical stimulus involved in sensory perception of bitter taste and protein targeting to membrane. Located in cytoplasm.

Source: NCBI Gene 83597 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 35 total
• MANE Select transcript: NM_031440

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15572
Approved symbol	RTP3
Name	receptor transporter protein 3
Location	3p21.31
Locus type	gene with protein product
Status	Approved
Aliases	LTM1, Z3CXXC3
Ensembl gene	ENSG00000163825
Ensembl biotype	protein_coding
OMIM	607181
Entrez	83597

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000296142, ENST00000684260

RefSeq mRNA: 1 — MANE Select: NM_031440 NM_031440

CCDS: CCDS2740

Canonical transcript exons

ENST00000296142 — 2 exons

Exon	Start	End
ENSE00001078635	46500356	46500950
ENSE00001317109	46497976	46498217

Expression profiles

Bgee: expression breadth broad, 49 present calls, max score 91.97.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2137 / max 112.5861, expressed in 8 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
36485	0.1409	8
36486	0.0729	7

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	91.97	gold quality
liver	UBERON:0002107	90.19	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.76	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.24	gold quality
epithelium of nasopharynx	UBERON:0001951	77.84	gold quality
secondary oocyte	CL:0000655	63.28	gold quality
mammary duct	UBERON:0001765	61.78	gold quality
buccal mucosa cell	CL:0002336	60.21	gold quality
parotid gland	UBERON:0001831	59.94	gold quality
vena cava	UBERON:0004087	59.56	gold quality
amniotic fluid	UBERON:0000173	58.71	gold quality
mucosa of paranasal sinus	UBERON:0005030	54.92	gold quality
oocyte	CL:0000023	54.80	gold quality
endothelial cell	CL:0000115	54.72	gold quality
gingival epithelium	UBERON:0001949	54.68	gold quality
skin of hip	UBERON:0001554	53.81	silver quality
esophagus squamous epithelium	UBERON:0006920	52.90	gold quality
gastrocnemius	UBERON:0001388	52.53	gold quality
cardia of stomach	UBERON:0001162	52.37	gold quality
sperm	CL:0000019	51.27	gold quality
pharyngeal mucosa	UBERON:0000355	51.19	gold quality
muscle of leg	UBERON:0001383	50.45	gold quality
gingiva	UBERON:0001828	50.42	gold quality
germinal epithelium of ovary	UBERON:0001304	50.32	gold quality
adult mammalian kidney	UBERON:0000082	50.17	gold quality
trachea	UBERON:0003126	48.81	gold quality
right testis	UBERON:0004534	48.25	gold quality
body of tongue	UBERON:0011876	46.77	gold quality
cerebellar vermis	UBERON:0004720	46.54	gold quality
dorsal root ganglion	UBERON:0000044	46.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 2)

• Loss of TMEM7 is associated with hepatocellular carcinoma (PMID:17693185)
• A common genetic variant, rs7430431 in the receptor transporting protein 3 (RTP3) gene, was identified in strong association with structural instability. (PMID:20175129)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Rtp3	ENSMUSG00000066319
rattus_norvegicus	Rtp3	ENSRNOG00000037167

Paralogs (4): RTP4 (ENSG00000136514), RTP1 (ENSG00000175077), RTP5 (ENSG00000188011), RTP2 (ENSG00000198471)

Protein

Protein identifiers

Receptor-transporting protein 3 — Q9BQQ7 (reviewed: Q9BQQ7)

Alternative names: 3CxxC-type zinc finger protein 3, Transmembrane protein 7

All UniProt accessions (1): Q9BQQ7

UniProt curated annotations — full annotation on UniProt →

Function. Promotes functional cell surface expression of the bitter taste receptors TAS2R16 and TAS2R43.

Subunit / interactions. Interacts with TAS2R16.

Subcellular location. Membrane.

Tissue specificity. Expressed predominantly in adult liver. Expressed in testis. Also expressed in kidney, lung and fetal liver. Low levels in heart, thyroid, adrenal gland, pancreas, ovary, prostate, skin, plasma leukocytes, bone marrow and fetal brain. Not detected in brain, spleen, colon, small intestine, skeletal muscle, stomach, placenta, salivary gland and uterus.

Similarity. Belongs to the TMEM7 family.

RefSeq proteins (1): NP_113628* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026096	R-trans_p	Family
IPR027377	ZAR1/RTP1-5-like_Znf-3CxxC	Domain

Pfam: PF13695

UniProt features (4 total): chain 1, topological domain 1, transmembrane region 1, zinc finger region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BQQ7-F1	78.33	0.58

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GOBP_PROTEIN_TARGETING, GOBP_SENSORY_PERCEPTION_OF_CHEMICAL_STIMULUS, TGACCTY_ERR1_Q2, COUP_01, GOBP_PROTEIN_TARGETING_TO_MEMBRANE, GOBP_DETECTION_OF_CHEMICAL_STIMULUS_INVOLVED_IN_SENSORY_PERCEPTION_OF_TASTE, GOBP_SENSORY_PERCEPTION_OF_TASTE, HNF4_DR1_Q3, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, HNF4_01, PPAR_DR1_Q2, GOBP_DETECTION_OF_STIMULUS, GOBP_SENSORY_PERCEPTION, GOMF_G_PROTEIN_COUPLED_RECEPTOR_BINDING, GOBP_MEMBRANE_ORGANIZATION

GO Biological Process (3): detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580), protein targeting to membrane (GO:0006612), protein insertion into membrane (GO:0051205)

GO Molecular Function (4): zinc ion binding (GO:0008270), olfactory receptor binding (GO:0031849), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): cytoplasm (GO:0005737), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
establishment of protein localization to membrane	2
cellular anatomical structure	2
detection of chemical stimulus involved in sensory perception of taste	1
sensory perception of bitter taste	1
protein targeting	1
intracellular protein localization	1
membrane organization	1
transition metal ion binding	1
G protein-coupled receptor binding	1
binding	1
cation binding	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

560 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RTP3	TMEM25	Q86YD3	571
RTP3	TAS2R20	P59543	567
RTP3	TMEM213	A2RRL7	528
RTP3	TMEM116	Q8NCL8	507
RTP3	LRRC2	Q9BYS8	480
RTP3	TAS2R1	Q9NYW7	480
RTP3	TMEM207	Q6UWW9	479
RTP3	NDC1	Q9BTX1	474
RTP3	TAS2R42	Q7RTR8	456
RTP3	TMEM61	Q8N0U2	440
RTP3	SLC35G2	Q8TBE7	432
RTP3	ANKUB1	A6NFN9	406
RTP3	REEP2	Q9BRK0	404
RTP3	TMEM45A	Q9NWC5	400
RTP3	HERC4	Q5GLZ8	387

IntAct

2 interactions, top by confidence:

A	B	Type	Score
RTP3	CASC3	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): PUM2 (Affinity Capture-MS), DIS3L2 (Affinity Capture-MS), CASC3 (Affinity Capture-MS), ELAVL2 (Affinity Capture-MS), HIST1H1A (Affinity Capture-MS), MOV10 (Affinity Capture-MS), PABPC4L (Affinity Capture-MS), APOBEC3F (Affinity Capture-MS)

ESM2 similar proteins: A0A0J9YX57, A0A0J9YY54, A0A494C086, A0A494C0Z2, A0A494C191, A0A494C1R9, A2A6M5, A2A9R3, A6NHP3, A6NIY4, A6NJR5, A6NKD2, A6NLX3, A6NNV3, B1AUS7, F6SZT2, O19110, P0C6Y7, P0CI01, P0CV98, P0CV99, P0CW00, P0CW01, P0DTA3, P0DUD1, P0DUD2, P0DUD3, P0DUD4, P0DUX0, P0DUX1, P0DV79, Q01534, Q12967, Q16666, Q495Y7, Q495Y8, Q587J8, Q5IBH6, Q5MJ68, Q5RD14

Diamond homologs: Q14D33, Q5QGT7, Q5QGU6, Q80ZI2, Q96DX8, Q9BQQ7, P59025, Q8C8C1, Q95JK0, Q9ER80

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	31
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

269 predictions. Top by Δscore:

Variant	Effect	Δscore
3:46497712:G:GT	donor_gain	0.9900
3:46498214:CCAG:C	donor_loss	0.9900
3:46498215:CAG:C	donor_loss	0.9900
3:46498216:AG:A	donor_loss	0.9900
3:46498217:GG:G	donor_loss	0.9900
3:46498218:GTGAG:G	donor_loss	0.9900
3:46498219:T:G	donor_loss	0.9900
3:46497669:A:T	donor_gain	0.9800
3:46497742:C:T	donor_gain	0.9700
3:46499371:G:GT	donor_gain	0.9400
3:46499375:G:GT	donor_gain	0.9400
3:46497746:T:TA	donor_gain	0.9300
3:46497747:AGAC:A	donor_gain	0.9300
3:46499376:A:T	donor_gain	0.9200
3:46498233:ATG:A	donor_gain	0.9100
3:46500278:T:TA	donor_gain	0.8900
3:46500279:A:AA	donor_gain	0.8900
3:46500352:ACAG:A	acceptor_loss	0.8900
3:46500353:CA:C	acceptor_loss	0.8900
3:46498414:GCC:G	donor_gain	0.8800
3:46499416:TCCC:T	donor_gain	0.8700
3:46498220:G:GT	donor_loss	0.8600
3:46500354:A:AG	acceptor_gain	0.8600
3:46500355:G:GG	acceptor_gain	0.8600
3:46500253:TC:T	donor_gain	0.8500
3:46497575:TCCC:T	donor_gain	0.8400
3:46500346:GTCTC:G	acceptor_loss	0.8300
3:46498213:GCCAG:G	donor_gain	0.8200
3:46499372:A:T	donor_gain	0.8200
3:46500347:TCTCC:T	acceptor_loss	0.8200

AlphaMissense

1543 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:46500357:T:C	F53L	0.987
3:46500359:C:A	F53L	0.987
3:46500359:C:G	F53L	0.987
3:46500411:T:C	F71L	0.972
3:46500413:C:A	F71L	0.972
3:46500413:C:G	F71L	0.972
3:46500465:T:C	F89L	0.970
3:46500467:T:A	F89L	0.970
3:46500467:T:G	F89L	0.970
3:46498135:T:A	W25R	0.965
3:46498135:T:C	W25R	0.965
3:46500358:T:C	F53S	0.963
3:46498137:G:C	W25C	0.962
3:46498137:G:T	W25C	0.962
3:46500386:G:C	W62C	0.954
3:46500386:G:T	W62C	0.954
3:46500516:T:C	F106L	0.949
3:46500518:C:A	F106L	0.949
3:46500518:C:G	F106L	0.949
3:46498210:T:C	F50L	0.947
3:46498212:C:A	F50L	0.947
3:46498212:C:G	F50L	0.947
3:46500358:T:G	F53C	0.940
3:46500517:T:C	F106S	0.938
3:46498136:G:C	W25S	0.934
3:46498096:T:C	F12L	0.933
3:46498098:T:A	F12L	0.933
3:46498098:T:G	F12L	0.933
3:46500473:G:C	Q91H	0.929
3:46500473:G:T	Q91H	0.929

dbSNP variants (sampled 300 via entrez): RS1000433942 (3:46496880 A>G), RS1001407635 (3:46499377 A>G), RS1002002127 (3:46500793 T>C), RS1002086287 (3:46496117 T>C), RS1002121092 (3:46501394 A>C), RS1002150729 (3:46501069 T>A), RS1003777809 (3:46499642 G>A), RS1004019227 (3:46497172 C>G), RS1004651826 (3:46498686 A>G), RS1004921509 (3:46498933 A>G), RS1006069507 (3:46500092 C>T), RS1006080934 (3:46499779 G>A), RS1007050526 (3:46500059 A>C), RS1007599048 (3:46496163 C>T), RS1008265453 (3:46498687 T>C)

Disease associations

OMIM: gene MIM:607181 | 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

18 total (human), top 18 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases expression, increases methylation	2
6-hydroxy-5-((p- sulfophenyl)azo)-2-naphthalenesulfonic acid disodium salt	affects cotreatment, increases expression	1
sodium arsenite	decreases expression	1
tebuconazole	decreases expression	1
CGP 52608	affects binding, increases reaction	1
obeticholic acid	increases expression	1
Leflunomide	increases expression	1
Cadmium	increases abundance, decreases expression	1
Chenodeoxycholic Acid	affects cotreatment, increases expression	1
Deoxycholic Acid	affects cotreatment, increases expression	1
Glycochenodeoxycholic Acid	affects cotreatment, increases expression	1
Glycocholic Acid	affects cotreatment, increases expression	1
Glycodeoxycholic Acid	increases expression, affects cotreatment	1
Smoke	increases expression	1
Valproic Acid	decreases methylation, increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression, increases abundance	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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