PRRT3

Summary

PRRT3 (proline rich transmembrane protein 3, HGNC:26591) is a protein-coding gene on chromosome 3p25.3, encoding Proline-rich transmembrane protein 3 (Q5FWE3).

Predicted to be located in membrane.

Source: NCBI Gene 285368 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 164 total
• MANE Select transcript: NM_207351

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26591
Approved symbol	PRRT3
Name	proline rich transmembrane protein 3
Location	3p25.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ33674
Ensembl gene	ENSG00000163704
Ensembl biotype	protein_coding
OMIM	619993
Entrez	285368

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 6 protein_coding, 2 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000295984, ENST00000411976, ENST00000412055, ENST00000707135, ENST00000707136, ENST00000879140, ENST00000879141, ENST00000879142, ENST00000911895

RefSeq mRNA: 2 — MANE Select: NM_207351 NM_001318871, NM_207351

CCDS: CCDS43049, CCDS82732

Canonical transcript exons

ENST00000412055 — 4 exons

Exon	Start	End
ENSE00001077487	9948758	9948913
ENSE00001288495	9949101	9950172
ENSE00001806810	9952322	9952408
ENSE00003998306	9945542	9948001

Expression profiles

Bgee: expression breadth ubiquitous, 175 present calls, max score 95.10.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.9942 / max 68.3234, expressed in 1256 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
41005	4.9942	1256

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
oviduct epithelium	UBERON:0004804	95.10	gold quality
endothelial cell	CL:0000115	87.16	silver quality
middle temporal gyrus	UBERON:0002771	86.02	gold quality
Brodmann (1909) area 23	UBERON:0013554	85.59	gold quality
buccal mucosa cell	CL:0002336	85.03	gold quality
primary visual cortex	UBERON:0002436	84.70	gold quality
prefrontal cortex	UBERON:0000451	84.14	gold quality
bronchial epithelial cell	CL:0002328	82.19	gold quality
right frontal lobe	UBERON:0002810	82.18	gold quality
frontal cortex	UBERON:0001870	82.09	gold quality
Brodmann (1909) area 9	UBERON:0013540	81.55	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	81.45	gold quality
neocortex	UBERON:0001950	81.30	gold quality
right hemisphere of cerebellum	UBERON:0014890	80.82	gold quality
bronchus	UBERON:0002185	80.76	gold quality
superior frontal gyrus	UBERON:0002661	80.17	gold quality
cerebellar hemisphere	UBERON:0002245	80.06	gold quality
cerebellar cortex	UBERON:0002129	80.04	gold quality
anterior cingulate cortex	UBERON:0009835	79.85	gold quality
adenohypophysis	UBERON:0002196	79.83	gold quality
caudate nucleus	UBERON:0001873	79.55	gold quality
cerebral cortex	UBERON:0000956	79.51	gold quality
nucleus accumbens	UBERON:0001882	79.49	gold quality
putamen	UBERON:0001874	79.42	gold quality
postcentral gyrus	UBERON:0002581	79.23	gold quality
cerebellum	UBERON:0002037	79.03	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.94	gold quality
pituitary gland	UBERON:0000007	78.88	gold quality
forebrain	UBERON:0001890	78.13	gold quality
entorhinal cortex	UBERON:0002728	77.75	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.62
E-MTAB-7303	no	452.50

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting PRRT3, 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-9-5P	100.00	72.28	2361
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-12133	99.92	71.82	2006
HSA-MIR-1271-5P	99.91	71.99	1972
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-548E-5P	99.89	72.73	4486
HSA-MIR-182-5P	99.87	74.03	2589
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-6844	99.82	70.69	2423
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-5004-5P	99.68	66.63	1294
HSA-MIR-504-3P	99.30	67.18	1745
HSA-MIR-6737-3P	98.95	68.56	1577
HSA-MIR-7157-3P	98.95	68.70	1582
HSA-MIR-10A-5P	98.89	69.85	712
HSA-MIR-10B-5P	98.89	69.86	711
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-10395-3P	98.10	66.70	1726
HSA-MIR-4305	97.94	68.63	533
HSA-MIR-3620-3P	97.78	64.88	772
HSA-MIR-6872-3P	97.08	66.99	750
HSA-MIR-4296	96.35	63.55	1233
HSA-MIR-4265	96.18	64.68	557
HSA-MIR-4322	96.18	64.85	539

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-14i3.2	ENSDARG00000097323
mus_musculus	Prrt3	ENSMUSG00000045009
rattus_norvegicus	Prrt3	ENSRNOG00000009863

Paralogs (1): PERM1 (ENSG00000187642)

Protein

Protein identifiers

Proline-rich transmembrane protein 3 — Q5FWE3 (reviewed: Q5FWE3)

All UniProt accessions (1): Q5FWE3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (3)

UniProt ID	Names	Canonical?
Q5FWE3-1	1	yes
Q5FWE3-2	2
Q5FWE3-3	3

RefSeq proteins (2): NP_001305800, NP_997234* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR043242	PRRT3	Family
IPR059081	PRRT3-4	Domain

Pfam: PF25987

UniProt features (54 total): modified residue 11, topological domain 8, transmembrane region 7, region of interest 6, compositionally biased region 6, sequence variant 5, glycosylation site 3, splice variant 3, sequence conflict 3, signal peptide 1, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5FWE3-F1	51.93	0.14

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (11): 777, 780, 789, 798, 808, 815, 854, 874, 902, 903, 911

Glycosylation sites (3): 329, 363, 379

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 55 (showing top): SP3_Q3, GOZGIT_ESR1_TARGETS_DN, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, TTTGCAC_MIR19A_MIR19B, IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM, NUYTTEN_EZH2_TARGETS_DN, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, NUYTTEN_NIPP1_TARGETS_DN, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, FORTSCHEGGER_PHF8_TARGETS_DN, CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

676 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRRT3	TEX51	A0A1B0GUA7	581
PRRT3	TATDN2	Q93075	570
PRRT3	PRRT2	Q7Z6L0	481
PRRT3	FANCD2OS	Q96PS1	479
PRRT3	SPRTN	Q9H040	478
PRRT3	ZZEF1	O43149	463
PRRT3	POLR3A	O14802	457
PRRT3	JAGN1	Q8N5M9	447
PRRT3	METTL27	Q8N6F8	409
PRRT3	EMC3	Q9P0I2	406
PRRT3	POLD1	P28340	406
PRRT3	CRELD1	Q96HD1	398
PRRT3	ERCC8	Q13216	395
PRRT3	TMEM86A	Q8N2M4	395
PRRT3	CPNE9	Q8IYJ1	395

IntAct

3 interactions, top by confidence:

A	B	Type	Score
PRRT3	PTPRD	psi-mi:“MI:0915”(physical association)	0.400
TMEM17	ESYT2	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (13): PRRT3 (Proximity Label-MS), PRRT3 (Affinity Capture-RNA), PTPRD (Affinity Capture-MS), PRRT3 (Affinity Capture-MS), PRRT3 (Affinity Capture-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS), PRRT3 (Proximity Label-MS)

ESM2 similar proteins: A0A0U1RRK4, A0A1W2PR82, A1YGK1, A2T7E6, A4D1S0, A6NEL2, A6QP24, A6QPM6, O43593, O43918, O94850, O95873, P0C7X2, P50617, P97609, Q3B7M4, Q3UM83, Q5FWE3, Q5JPB2, Q5M844, Q5XJV6, Q61645, Q64322, Q6GQX2, Q6NZ36, Q6PE13, Q6UWD8, Q6ZMS7, Q6ZW13, Q76NI1, Q7Z6P3, Q8BWG4, Q8BZW2, Q8IWN7, Q8NBB4, Q8NDX1, Q8NHY3, Q8TBC5, Q8TER5, Q91XA5

Diamond homologs: B2RU40, C9JH25, D4A9R4, Q5FWE3, Q6PE13

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	153
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1497 predictions. Top by Δscore:

Variant	Effect	Δscore
3:9942940:G:GT	donor_gain	1.0000
3:9943075:A:AG	acceptor_gain	1.0000
3:9943076:G:GG	acceptor_gain	1.0000
3:9943076:GACT:G	acceptor_gain	1.0000
3:9943377:CAAG:C	acceptor_loss	1.0000
3:9943378:A:AG	acceptor_gain	1.0000
3:9943378:AAG:A	acceptor_loss	1.0000
3:9943378:AAGAT:A	acceptor_gain	1.0000
3:9943379:A:G	acceptor_gain	1.0000
3:9943379:AGAT:A	acceptor_gain	1.0000
3:9943379:AGATG:A	acceptor_loss	1.0000
3:9943380:G:GA	acceptor_gain	1.0000
3:9943380:GAT:G	acceptor_gain	1.0000
3:9943380:GATG:G	acceptor_gain	1.0000
3:9943380:GATGT:G	acceptor_gain	1.0000
3:9943512:CCAGG:C	donor_loss	1.0000
3:9943513:CAGGT:C	donor_loss	1.0000
3:9943515:GGT:G	donor_loss	1.0000
3:9943516:G:GG	donor_gain	1.0000
3:9944363:A:AG	acceptor_gain	1.0000
3:9944364:G:GG	acceptor_gain	1.0000
3:9944364:GA:G	acceptor_gain	1.0000
3:9948914:C:CC	acceptor_gain	1.0000
3:9949097:CCA:C	donor_loss	1.0000
3:9949098:CAC:C	donor_loss	1.0000
3:9949099:ACCTG:A	donor_loss	1.0000
3:9940845:CACA:C	acceptor_loss	0.9900
3:9940848:A:AG	acceptor_gain	0.9900
3:9940849:G:GA	acceptor_gain	0.9900
3:9940849:GC:G	acceptor_gain	0.9900

AlphaMissense

6149 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:9946726:A:T	I816N	0.998
3:9947760:C:A	W471C	0.998
3:9947760:C:G	W471C	0.998
3:9946726:A:C	I816S	0.996
3:9946728:G:C	S815R	0.996
3:9946728:G:T	S815R	0.996
3:9946730:T:G	S815R	0.996
3:9946738:A:T	L812Q	0.996
3:9947762:A:G	W471R	0.996
3:9947762:A:T	W471R	0.996
3:9946237:A:T	I979N	0.995
3:9946738:A:G	L812P	0.995
3:9947793:C:A	W460C	0.995
3:9947793:C:G	W460C	0.995
3:9946432:A:G	I914T	0.994
3:9946744:A:T	I810N	0.994
3:9947220:G:C	S651R	0.993
3:9947220:G:T	S651R	0.993
3:9947222:T:G	S651R	0.993
3:9946714:A:T	L820H	0.992
3:9946723:T:A	D817V	0.992
3:9946744:A:C	I810S	0.992
3:9946237:A:C	I979S	0.991
3:9946726:A:G	I816T	0.991
3:9946744:A:G	I810T	0.991
3:9947147:A:G	W676R	0.991
3:9947147:A:T	W676R	0.991
3:9947160:G:C	F671L	0.991
3:9947160:G:T	F671L	0.991
3:9947162:A:G	F671L	0.991

dbSNP variants (sampled 300 via entrez): RS1000684092 (3:9945168 A>G), RS1001222286 (3:9945613 T>G), RS1001307028 (3:9952814 G>A), RS1002762606 (3:9945492 C>T), RS1002876658 (3:9946198 G>A,C), RS1002947082 (3:9945927 C>G), RS1003166413 (3:9952038 G>A,C,T), RS1003206006 (3:9950502 CT>C), RS1003210002 (3:9947611 A>G,T), RS1003285449 (3:9947222 T>A,C), RS1003290019 (3:9945169 A>G), RS1003729986 (3:9950191 A>G), RS1003908004 (3:9953262 T>G), RS1004706329 (3:9950878 C>G,T), RS1005216456 (3:9947489 C>T)

Disease associations

OMIM: gene MIM:619993 | 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

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, increases expression	4
Smoke	decreases expression, increases expression	2
Tobacco Smoke Pollution	decreases expression	2
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
ferrous chloride	decreases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, decreases expression	1
pentabromodiphenyl ether	decreases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	increases expression	1
ICG 001	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
Sunitinib	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	affects methylation, decreases methylation	1
Coumestrol	affects cotreatment, decreases expression	1
Dexamethasone	increases expression	1
Doxorubicin	affects expression	1
Estradiol	affects cotreatment, decreases expression	1
Hydrogen Peroxide	affects expression	1
Aflatoxin B1	increases expression	1
Copper Sulfate	decreases expression	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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