P3R3URF

Summary

P3R3URF (PIK3R3 upstream open reading frame, HGNC:53451) is a protein-coding gene on chromosome 1p34.1, encoding PIK3R3 upstream open reading frame protein (A0A087WWA1).

Predicted to be involved in cytokine-mediated signaling pathway.

Source: NCBI Gene 110117498 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001328655

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53451
Approved symbol	P3R3URF
Name	PIK3R3 upstream open reading frame
Location	1p34.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000250719
Ensembl biotype	protein_coding
Entrez	110117498

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000506599

RefSeq mRNA: 1 — MANE Select: NM_001328655 NM_001328655

CCDS: CCDS85970

Canonical transcript exons

ENST00000506599 — 2 exons

Exon	Start	End
ENSE00002042368	46176228	46176488
ENSE00002064464	46175486	46175629

Expression profiles

Bgee: expression breadth broad, 62 present calls, max score 96.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0829 / max 79.8420, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
12165	0.0829	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	96.87	gold quality
right testis	UBERON:0004534	96.69	gold quality
testis	UBERON:0000473	96.06	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.02	gold quality
mucosa of transverse colon	UBERON:0004991	50.85	gold quality
metanephros cortex	UBERON:0010533	43.60	gold quality
granulocyte	CL:0000094	43.36	silver quality
hindlimb stylopod muscle	UBERON:0004252	38.38	gold quality
sural nerve	UBERON:0015488	37.98	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
adenohypophysis	UBERON:0002196	35.37	gold quality
right hemisphere of cerebellum	UBERON:0014890	35.23	silver quality
right adrenal gland cortex	UBERON:0035827	33.96	silver quality
right adrenal gland	UBERON:0001233	33.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
cortex of kidney	UBERON:0001225	32.52	gold quality
tonsil	UBERON:0002372	32.21	silver quality
right coronary artery	UBERON:0001625	32.10	silver quality
bone marrow	UBERON:0002371	31.74	gold quality
pituitary gland	UBERON:0000007	31.31	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
prefrontal cortex	UBERON:0000451	29.31	silver quality
adrenal gland	UBERON:0002369	29.21	gold quality
left adrenal gland	UBERON:0001234	28.91	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.98
E-ANND-3	no	0.06

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	P3r3urf	ENSMUSG00000078593
rattus_norvegicus	P3r3urf	ENSRNOG00000049874

Protein

Protein identifiers

PIK3R3 upstream open reading frame protein — A0A087WWA1 (reviewed: A0A087WWA1)

All UniProt accessions (1): A0A087WWA1

RefSeq proteins (1): NP_001315584* (*=MANE)

Domains & families (InterPro)

UniProt features (2 total): chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A087WWA1-F1	60.96	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 7 (showing top): GOBP_RESPONSE_TO_PEPTIDE, chr1p34, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, DACH1_TARGET_GENES, GLI1_TARGET_GENES, BDP1_TARGET_GENES, GOBP_CYTOKINE_MEDIATED_SIGNALING_PATHWAY

GO Biological Process (1): cytokine-mediated signaling pathway (GO:0019221)

GO Molecular Function (0):

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cell surface receptor signaling pathway	1
cellular response to cytokine stimulus	1

Protein interactions and networks

STRING

78 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
P3R3URF	RBBP6	Q7Z6E9	216
P3R3URF	ATG5	Q9H1Y0	206
P3R3URF	PDPK1	O15530	192
P3R3URF	IL5	P05113	187
P3R3URF	OCSTAMP	Q9BR26	166
P3R3URF	ATF1	P18846	162
P3R3URF	CREB1	P16220	162
P3R3URF	LXN	Q9BS40	160
P3R3URF	PIK3CA	P42336	159
P3R3URF	PIK3CD	O00329	159
P3R3URF	PIK3CG	P48736	159
P3R3URF	PIK3CB	P42338	159
P3R3URF	PIK3C2A	O00443	90
P3R3URF	PIK3C2B	O00750	90
P3R3URF	PIK3C2G	O75747	90

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A087WWA1, A0A182BSS5, B1AUF7, D3DTV9, K8DWB5, O12987, O12995, O13557, O30006, O83592, P01073, P03124, P03846, P05679, P08771, P0C5P1, P0C841, P0CV22, P10437, P14311, P16773, P18455, P20218, P23183, P34245, P36283, P38303, P39978, P40519, P53194, P75320, P75602, P81056, P89888, Q04413, Q0UI01, Q28UQ5, Q31CC8, Q3BSH4, Q3E789

Diamond homologs: A0A087WWA1, B1AUF7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

90 predictions. Top by Δscore:

Variant	Effect	Δscore
1:46176284:ATGGC:A	donor_gain	0.9900
1:46175630:C:CC	acceptor_gain	0.9800
1:46175724:T:TA	donor_gain	0.9600
1:46176222:GCTAA:G	donor_loss	0.9500
1:46176223:CTAA:C	donor_loss	0.9500
1:46176224:TAACC:T	donor_loss	0.9500
1:46176225:AACCT:A	donor_loss	0.9500
1:46176226:A:G	donor_loss	0.9500
1:46176227:C:CA	donor_loss	0.9500
1:46175627:GAA:G	acceptor_gain	0.9300
1:46175629:ACTG:A	acceptor_gain	0.9200
1:46176284:ATGG:A	donor_gain	0.9200
1:46176228:C:G	donor_loss	0.9100
1:46175627:GAACT:G	acceptor_gain	0.9000
1:46175628:AACTG:A	acceptor_gain	0.9000
1:46175630:C:CA	acceptor_loss	0.9000
1:46175630:CTGA:C	acceptor_gain	0.9000
1:46175625:GAGAA:G	acceptor_gain	0.8900
1:46175631:T:A	acceptor_gain	0.8900
1:46175628:AA:A	acceptor_gain	0.8800
1:46175626:AGAA:A	acceptor_gain	0.8600
1:46175626:AGAAC:A	acceptor_gain	0.8600
1:46175737:T:TA	donor_gain	0.7800
1:46176217:C:CA	donor_gain	0.7800
1:46176229:T:C	donor_loss	0.7800
1:46175624:TGAGA:T	acceptor_gain	0.7600
1:46176221:GGCT:G	donor_loss	0.7000
1:46176282:CCA:C	donor_gain	0.6500
1:46175625:GAGA:G	acceptor_gain	0.6200
1:46175740:T:TA	donor_gain	0.6000

AlphaMissense

613 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:46176367:G:C	F35L	0.921
1:46176367:G:T	F35L	0.921
1:46176369:A:G	F35L	0.921
1:46176364:C:A	K36N	0.815
1:46176364:C:G	K36N	0.815
1:46176358:G:C	S38R	0.808
1:46176358:G:T	S38R	0.808
1:46176360:T:G	S38R	0.808
1:46176379:A:C	F31L	0.807
1:46176379:A:T	F31L	0.807
1:46176381:A:G	F31L	0.807
1:46175590:A:T	L95H	0.785
1:46175598:A:C	F92L	0.767
1:46175598:A:T	F92L	0.767
1:46175600:A:G	F92L	0.767
1:46176370:C:A	M34I	0.712
1:46176370:C:G	M34I	0.712
1:46176370:C:T	M34I	0.712
1:46176368:A:G	F35S	0.702
1:46176365:T:A	K36M	0.687
1:46176368:A:C	F35C	0.675
1:46176352:T:A	R40S	0.670
1:46176352:T:G	R40S	0.670
1:46176369:A:T	F35I	0.645
1:46175593:A:G	I94T	0.639
1:46176242:A:G	I77T	0.639
1:46176359:C:T	S38N	0.639
1:46176371:A:G	M34T	0.624
1:46176366:T:C	K36E	0.622
1:46176359:C:A	S38I	0.616

dbSNP variants (sampled 300 via entrez): RS1000053163 (1:46176126 T>C), RS1000804489 (1:46176440 C>T), RS1001153534 (1:46176708 G>T), RS1001454678 (1:46176635 G>A,C), RS1001791600 (1:46175773 C>T), RS1002458914 (1:46178208 T>C), RS1003872942 (1:46176091 G>A,T), RS1004039016 (1:46178339 A>G), RS1004310354 (1:46176021 T>C), RS1006326987 (1:46177209 C>T), RS1006625635 (1:46177377 A>G), RS1007772123 (1:46177423 C>A), RS1008621693 (1:46175081 G>A), RS1010096830 (1:46176603 G>C,T), RS1010584766 (1:46176356 C>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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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