PRRT4

Summary

PRRT4 (proline rich transmembrane protein 4, HGNC:37280) is a protein-coding gene on chromosome 7q32.1, encoding Proline-rich transmembrane protein 4 (C9JH25).

Predicted to be located in membrane.

Source: NCBI Gene 401399 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 172 total
• MANE Select transcript: NM_001174164

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37280
Approved symbol	PRRT4
Name	proline rich transmembrane protein 4
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000224940
Ensembl biotype	protein_coding
Entrez	401399

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000446477, ENST00000480290, ENST00000489517, ENST00000489835, ENST00000495931, ENST00000535159, ENST00000851338

RefSeq mRNA: 8 — MANE Select: NM_001174164 NM_001114726, NM_001174164, NM_001395429, NM_001405492, NM_001405493, NM_001405494, NM_001405495, NM_001405496

CCDS: CCDS47698, CCDS55160

Canonical transcript exons

ENST00000446477 — 6 exons

Exon	Start	End
ENSE00001606539	128361561	128361690
ENSE00001708729	128359340	128360063
ENSE00001753606	128359149	128359253
ENSE00001761020	128358681	128358800
ENSE00001770606	128350325	128352678
ENSE00001849895	128361306	128361422

Expression profiles

Bgee: expression breadth ubiquitous, 125 present calls, max score 90.87.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7089 / max 169.4031, expressed in 223 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
86058	0.2713	98
86055	0.1577	66
86059	0.1234	41
86057	0.1018	46
86056	0.0547	23

Top tissues by expression

131 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	90.87	gold quality
bone marrow	UBERON:0002371	84.12	gold quality
omental fat pad	UBERON:0010414	78.81	gold quality
cortical plate	UBERON:0005343	78.09	gold quality
hindlimb stylopod muscle	UBERON:0004252	77.71	gold quality
adipose tissue	UBERON:0001013	77.09	gold quality
bone marrow cell	CL:0002092	76.18	gold quality
subcutaneous adipose tissue	UBERON:0002190	75.61	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.01	gold quality
cerebellar hemisphere	UBERON:0002245	73.99	gold quality
cerebellum	UBERON:0002037	73.88	gold quality
cerebellar cortex	UBERON:0002129	73.87	gold quality
hypothalamus	UBERON:0001898	73.84	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	73.56	gold quality
nucleus accumbens	UBERON:0001882	72.72	gold quality
right frontal lobe	UBERON:0002810	70.84	gold quality
anterior cingulate cortex	UBERON:0009835	70.38	gold quality
frontal cortex	UBERON:0001870	69.73	gold quality
primary visual cortex	UBERON:0002436	69.60	gold quality
caudate nucleus	UBERON:0001873	69.38	gold quality
prefrontal cortex	UBERON:0000451	69.31	gold quality
skeletal muscle tissue	UBERON:0001134	68.74	gold quality
superior frontal gyrus	UBERON:0002661	68.34	gold quality
cerebral cortex	UBERON:0000956	68.25	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	68.04	gold quality
lower esophagus mucosa	UBERON:0035834	67.89	gold quality
apex of heart	UBERON:0002098	67.61	gold quality
Brodmann (1909) area 9	UBERON:0013540	67.45	gold quality
thoracic mammary gland	UBERON:0005200	67.34	gold quality
mucosa of stomach	UBERON:0001199	66.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.26

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting PRRT4, 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-513A-5P	100.00	69.77	2465
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-6772-5P	99.94	67.01	577
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-137-3P	99.87	74.74	2401
HSA-MIR-383-3P	99.85	65.84	1359
HSA-MIR-3663-3P	99.84	70.39	798
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-6764-5P	99.75	67.89	2304
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-1915-3P	99.58	66.79	1988
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-133A-5P	99.28	69.13	941
HSA-MIR-544B	99.18	67.41	1632
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-6830-5P	99.01	68.73	1884
HSA-MIR-331-3P	98.76	64.91	793
HSA-MIR-2467-3P	98.65	67.18	1969
HSA-MIR-1301-3P	98.64	68.27	1071
HSA-MIR-5047	98.64	68.62	1035
HSA-MIR-323A-5P	98.59	65.13	651
HSA-MIR-1199-5P	98.44	66.51	829
HSA-MIR-6751-3P	98.44	66.35	835

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	prrt4a	ENSDARG00000088343
danio_rerio	prrt4b	ENSDARG00000099812
mus_musculus	Prrt4	ENSMUSG00000079654
rattus_norvegicus	Prrt4	ENSRNOG00000039388

Protein

Protein identifiers

Proline-rich transmembrane protein 4 — C9JH25 (reviewed: C9JH25)

All UniProt accessions (4): C9JH25, C9JVX5, C9JWH6, H7C4Q3

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Isoforms (3)

UniProt ID	Names	Canonical?
C9JH25-1	1	yes
C9JH25-2	2
C9JH25-3	3

RefSeq proteins (8): NP_001108198, NP_001167635, NP_001382358, NP_001392421, NP_001392422, NP_001392423, NP_001392424, NP_001392425 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052836	PRRT_domain-containing	Family
IPR059081	PRRT3-4	Domain

Pfam: PF25987

UniProt features (16 total): transmembrane region 5, region of interest 4, splice variant 3, signal peptide 1, chain 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-C9JH25-F1	53.14	0.11

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 (1): 641

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): chr7q32, ZNF322_TARGET_GENES, ZNF563_TARGET_GENES, MIR6764_5P, MIR6830_5P, MIR3065_3P, MIR138_5P, MIR1915_3P, MIR5189_3P, GSE14350_TREG_VS_TEFF_IN_IL2RB_KO_DN, MANNO_MIDBRAIN_NEUROTYPES_HDA1, MANNO_MIDBRAIN_NEUROTYPES_HDA2, MANNO_MIDBRAIN_NEUROTYPES_HGABA, MANNO_MIDBRAIN_NEUROTYPES_HSERT, ZSCAN4_TARGET_GENES

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

186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRRT4	KIAA0825	Q8IV33	474
PRRT4	RBM28	Q9NW13	448
PRRT4	ANKDD1B	A6NHY2	447
PRRT4	ARMH4	Q86TY3	434
PRRT4	SMIM1	B2RUZ4	430
PRRT4	KLHDC8A	Q8IYD2	417
PRRT4	ZNF300	Q96RE9	399
PRRT4	TMEM209	Q96SK2	398
PRRT4	SPATA17	Q96L03	372
PRRT4	KLHDC10	Q6PID8	370
PRRT4	PRSS56	P0CW18	324
PRRT4	UBR7	Q8N806	323
PRRT4	HEMGN	Q9BXL5	308
PRRT4	SFXN1	Q9H9B4	307
PRRT4	TSGA13	Q96PP4	307

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CEACAM8	PRRT4	psi-mi:“MI:0914”(association)	0.350
SLC7A1	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (17): PRRT4 (Affinity Capture-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Proximity Label-MS), PRRT4 (Affinity Capture-MS), PRRT4 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0U1RQ45, A0A0U1RQS6, A0A2R8YCJ5, A2A699, A2AEV7, A6NGB7, A6NJG2, A6NKF7, A6NKL6, A6NL88, A8MVW0, A9JSM3, B2RU40, B8ZZ34, C9JH25, D4A9R4, J3QNX5, P0CG09, P98077, Q0VD38, Q14761, Q17QH7, Q29RK8, Q2KJ18, Q2M3V2, Q3SX20, Q5BJT1, Q5HZJ5, Q5RKR3, Q5T442, Q64697, Q69YZ2, Q6PB97, Q6PCT2, Q6UXK2, Q6ZMQ8, Q6ZVH7, Q6ZW31, Q80XF7, Q8BLS7

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	159
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1036 predictions. Top by Δscore:

Variant	Effect	Δscore
7:128359147:AC:A	donor_gain	1.0000
7:128359148:CC:C	donor_gain	1.0000
7:128351295:T:TA	donor_gain	0.9900
7:128358679:A:AC	donor_gain	0.9900
7:128358680:C:CC	donor_gain	0.9900
7:128358797:AACCC:A	acceptor_loss	0.9900
7:128358799:CC:C	acceptor_gain	0.9900
7:128358799:CCCT:C	acceptor_loss	0.9900
7:128358800:CC:C	acceptor_gain	0.9900
7:128358800:CCTGC:C	acceptor_loss	0.9900
7:128358801:C:CA	acceptor_loss	0.9900
7:128358802:T:C	acceptor_loss	0.9900
7:128359141:AAACT:A	donor_loss	0.9900
7:128359142:AACTC:A	donor_loss	0.9900
7:128359143:ACTC:A	donor_loss	0.9900
7:128359144:CTCAC:C	donor_loss	0.9900
7:128359145:TCACC:T	donor_loss	0.9900
7:128359146:CACCC:C	donor_loss	0.9900
7:128359147:A:AC	donor_gain	0.9900
7:128359147:A:AG	donor_loss	0.9900
7:128359148:C:CC	donor_gain	0.9900
7:128359251:ATCCT:A	acceptor_loss	0.9900
7:128359252:TC:T	acceptor_gain	0.9900
7:128359253:CC:C	acceptor_gain	0.9900
7:128359253:CCTGC:C	acceptor_loss	0.9900
7:128359254:C:CC	acceptor_gain	0.9900
7:128359254:CT:C	acceptor_loss	0.9900
7:128359255:T:A	acceptor_loss	0.9900
7:128359336:TCACC:T	donor_loss	0.9900
7:128359337:CA:C	donor_loss	0.9900

AlphaMissense

5577 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:128351363:G:C	S731R	0.995
7:128351363:G:T	S731R	0.995
7:128351365:T:G	S731R	0.995
7:128352467:C:A	W363C	0.995
7:128352467:C:G	W363C	0.995
7:128351361:A:T	I732N	0.993
7:128351379:A:G	I726T	0.989
7:128351379:A:T	I726N	0.989
7:128351353:C:G	A735P	0.987
7:128351373:A:G	L728P	0.987
7:128351373:A:T	L728Q	0.987
7:128352469:A:G	W363R	0.987
7:128352469:A:T	W363R	0.987
7:128352500:C:A	W352C	0.987
7:128352500:C:G	W352C	0.987
7:128350883:G:C	S891R	0.986
7:128350883:G:T	S891R	0.986
7:128350885:T:G	S891R	0.986
7:128351379:A:C	I726S	0.986
7:128351762:C:A	W598C	0.986
7:128351762:C:G	W598C	0.986
7:128351764:A:G	W598R	0.986
7:128351764:A:T	W598R	0.986
7:128350874:G:C	S894R	0.983
7:128350874:G:T	S894R	0.983
7:128350876:T:G	S894R	0.983
7:128352434:G:C	F374L	0.983
7:128352434:G:T	F374L	0.983
7:128352436:A:G	F374L	0.983
7:128351361:A:C	I732S	0.982

dbSNP variants (sampled 300 via entrez): RS1000192806 (7:128363879 G>T), RS1000265279 (7:128359470 G>A,T), RS1000301275 (7:128359785 G>A), RS1000350498 (7:128359583 C>T), RS1000739643 (7:128360549 G>C), RS1000881896 (7:128353180 T>G), RS1001159004 (7:128355723 T>G), RS1001272511 (7:128360845 G>A,T), RS1001278015 (7:128354329 C>T), RS1001855643 (7:128354122 A>G), RS1002746413 (7:128362829 A>G), RS1002815498 (7:128351939 T>C,G), RS1002819886 (7:128361701 C>T), RS1002821034 (7:128357665 G>C), RS1002829208 (7:128357325 G>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
(+)-JQ1 compound	decreases expression	2
FR900359	decreases phosphorylation	1
propionaldehyde	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
abrine	decreases expression	1
Sunitinib	decreases expression	1
Aldehydes	increases expression	1
Benzo(a)pyrene	increases methylation	1
Endosulfan	increases expression	1
Testosterone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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