PRR3

Summary

PRR3 (proline rich 3, HGNC:21149) is a protein-coding gene on chromosome 6p21.33, encoding Proline-rich protein 3 (P79522).

Enables RNA binding activity.

Source: NCBI Gene 80742 — RefSeq curated summary.

At a glance

• GWAS associations: 19
• Clinical variants (ClinVar): 39 total
• MANE Select transcript: NM_025263

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:21149
Approved symbol	PRR3
Name	proline rich 3
Location	6p21.33
Locus type	gene with protein product
Status	Approved
Aliases	CAT56, Em:AB014077.1, Em:AB023052.2
Ensembl gene	ENSG00000204576
Ensembl biotype	protein_coding
Entrez	80742

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 3 protein_coding, 2 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000376557, ENST00000376560, ENST00000470703, ENST00000481741, ENST00000491173, ENST00000498336, ENST00000934408

RefSeq mRNA: 2 — MANE Select: NM_025263 NM_001077497, NM_025263

CCDS: CCDS43440, CCDS43441

Canonical transcript exons

ENST00000376560 — 4 exons

Exon	Start	End
ENSE00001876281	30557295	30557450
ENSE00003578614	30561834	30562124
ENSE00003671319	30558150	30558212
ENSE00003901246	30562389	30563723

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 93.54.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.0091 / max 224.3093, expressed in 1808 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter ID	TPM avg	Samples expressed
66737	19.4776	1793
66734	1.8485	893
66736	1.7004	953
66735	0.8888	369
66733	0.7072	340
66739	0.2985	137
66732	0.0883	34

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	93.54	gold quality
ganglionic eminence	UBERON:0004023	92.30	gold quality
cerebellar hemisphere	UBERON:0002245	89.80	gold quality
cerebellar cortex	UBERON:0002129	89.76	gold quality
cerebellum	UBERON:0002037	89.67	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.60	gold quality
left ovary	UBERON:0002119	88.95	gold quality
ovary	UBERON:0000992	88.84	gold quality
right ovary	UBERON:0002118	88.40	gold quality
ventricular zone	UBERON:0003053	88.15	gold quality
superior frontal gyrus	UBERON:0002661	87.10	gold quality
Brodmann (1909) area 9	UBERON:0013540	87.10	gold quality
endocervix	UBERON:0000458	87.07	gold quality
pituitary gland	UBERON:0000007	86.73	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	86.69	gold quality
adenohypophysis	UBERON:0002196	86.57	gold quality
body of uterus	UBERON:0009853	86.56	gold quality
hypothalamus	UBERON:0001898	86.42	gold quality
primary visual cortex	UBERON:0002436	86.28	gold quality
right frontal lobe	UBERON:0002810	86.25	gold quality
anterior cingulate cortex	UBERON:0009835	86.08	gold quality
endometrium	UBERON:0001295	85.99	gold quality
nucleus accumbens	UBERON:0001882	85.89	gold quality
caudate nucleus	UBERON:0001873	85.67	gold quality
lymph node	UBERON:0000029	85.63	gold quality
fallopian tube	UBERON:0003889	85.33	gold quality
putamen	UBERON:0001874	85.31	gold quality
uterine cervix	UBERON:0000002	85.30	gold quality
brain	UBERON:0000955	85.29	gold quality
Ammon’s horn	UBERON:0001954	85.25	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.67

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

94 targeting PRR3, 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-4425	100.00	67.59	1049
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-34A-5P	99.99	71.21	1784
HSA-MIR-449A	99.99	71.05	1776
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-27A-3P	99.98	72.13	2955
HSA-MIR-27B-3P	99.98	72.13	2955
HSA-MIR-9985	99.98	72.11	2939
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-4271	99.88	68.32	2244
HSA-MIR-3919	99.87	69.45	2489
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-5582-3P	99.86	72.48	4221
HSA-MIR-629-3P	99.85	67.99	1875
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-370-5P	99.78	66.81	706
HSA-MIR-556-3P	99.74	68.75	1203

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prr3	ENSMUSG00000038500

Paralogs (2): ZC3H18 (ENSG00000158545), PPP1R10 (ENSG00000204569)

Protein

Protein identifiers

Proline-rich protein 3 — P79522 (reviewed: P79522)

Alternative names: MHC class I region proline-rich protein CAT56

All UniProt accessions (2): P79522, Q96QB9

Isoforms (2)

UniProt ID	Names	Canonical?
P79522-1	1	yes
P79522-2	2

RefSeq proteins (2): NP_001070965, NP_079539* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000571	Znf_CCCH	Domain
IPR036855	Znf_CCCH_sf	Homologous_superfamily
IPR042805	PRR3	Family

Pfam: PF00642

UniProt features (9 total): compositionally biased region 4, chain 1, zinc finger region 1, region of interest 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-P79522-F1	61.18	0.06

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 190 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE45365_NK_CELL_VS_CD8_TCELL_UP, ATF_B, TGGTGCT_MIR29A_MIR29B_MIR29C, BROWNE_HCMV_INFECTION_6HR_DN, GOBP_DNA_TEMPLATED_TRANSCRIPTION_TERMINATION, CMYB_01, CREBP1_Q2, GOBP_POSITIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, PUJANA_CHEK2_PCC_NETWORK, CREB_Q4, GTGCCTT_MIR506, BROWNE_HCMV_INFECTION_48HR_DN, E4F1_Q6

GO Biological Process (0):

GO Molecular Function (4): RNA binding (GO:0003723), zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleic acid binding	1
transition metal ion binding	1
binding	1
cation binding	1

Protein interactions and networks

STRING

870 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR3	MUCL3	Q3MIW9	539
PRR3	PPP1R11	O60927	522
PRR3	MRPS18B	Q9Y676	505
PRR3	TRIM10	Q9UDY6	453
PRR3	C5orf22	Q49AR2	448
PRR3	GNL1	P36915	448
PRR3	TRIM26	Q12899	437
PRR3	DHX16	O60231	415
PRR3	TRIM39	Q9HCM9	367
PRR3	SUPT7L	O94864	354
PRR3	PPP1R18	Q6NYC8	349
PRR3	RRM1	P23921	348
PRR3	SNRPE	P08578	346
PRR3	PLRG1	O43660	343
PRR3	LILRA2	Q8N149	342

IntAct

122 interactions, top by confidence:

A	B	Type	Score
RBMY1F	PRR3	psi-mi:“MI:0915”(physical association)	0.780
PRR3	RBMY1F	psi-mi:“MI:0915”(physical association)	0.780
PRR3	HNRNPK	psi-mi:“MI:0915”(physical association)	0.740
HNRNPK	PRR3	psi-mi:“MI:0915”(physical association)	0.740
PRR3	RBMX	psi-mi:“MI:0915”(physical association)	0.720
KHDRBS2	PRR3	psi-mi:“MI:0915”(physical association)	0.720
PRR3	ASF1A	psi-mi:“MI:0915”(physical association)	0.720
RBMX	PRR3	psi-mi:“MI:0915”(physical association)	0.720
PRR3	KHDRBS2	psi-mi:“MI:0915”(physical association)	0.720
ASF1A	PRR3	psi-mi:“MI:0915”(physical association)	0.720
KHDRBS3	PRR3	psi-mi:“MI:0915”(physical association)	0.670
PRR3	RBMY1A1	psi-mi:“MI:0915”(physical association)	0.560
PSMA3	PRR3	psi-mi:“MI:0915”(physical association)	0.560
TLE5	PRR3	psi-mi:“MI:0915”(physical association)	0.560
PRR3	CCDC57	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (273): PRR3 (Two-hybrid), PRR3 (Two-hybrid), PRR3 (Two-hybrid), PRR3 (Two-hybrid), PRR3 (Two-hybrid), PRR3 (Two-hybrid), RBMY1F (Two-hybrid), KHDRBS2 (Two-hybrid), CCDC57 (Two-hybrid), PRR3 (Affinity Capture-MS), PRR3 (Affinity Capture-MS), PRR3 (Affinity Capture-MS), PRR3 (Affinity Capture-MS), PRR3 (Affinity Capture-MS), PRR3 (Affinity Capture-MS)

ESM2 similar proteins: A3RK75, A5X7A0, A7XYH5, A7XYH9, A7XYI6, A7XYQ1, E7F888, E9PT37, E9Q2Z1, P0DW16, P48634, P61129, P79522, P98177, Q08D57, Q0P5V2, Q1LY77, Q1RNF8, Q3UQS8, Q4R7I8, Q5F3P8, Q5JSZ5, Q5T481, Q5TM26, Q5VK71, Q63014, Q66J90, Q6MG07, Q6MG48, Q6PJG2, Q75N03, Q767L1, Q7TPM1, Q7TSC1, Q7YR36, Q811B5, Q8BYK8, Q8C208, Q8CFT2, Q96EV2

Diamond homologs: O55000, P79522, Q5TM61, Q6GLQ4, Q6MG07, Q767K9, Q767L1, Q7YR36, Q7YR38, Q80W00, Q811B5, Q96QC0

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 54 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO term	Partners	Fold	FDR
regulation of alternative mRNA splicing, via spliceosome	5	24.9×	3e-04
mRNA processing	7	11.2×	3e-04
RNA splicing	6	10.8×	1e-03
translation	5	10.5×	6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	26
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

493 predictions. Top by Δscore:

Variant	Effect	Δscore
6:30557435:G:GT	donor_gain	1.0000
6:30557439:G:GT	donor_gain	1.0000
6:30557439:G:T	donor_gain	1.0000
6:30557414:G:GT	donor_gain	0.9900
6:30557414:G:T	donor_gain	0.9900
6:30557424:GAGA:G	donor_gain	0.9900
6:30557427:A:G	donor_gain	0.9900
6:30557432:G:GT	donor_gain	0.9900
6:30557468:G:T	donor_gain	0.9900
6:30561505:GACT:G	donor_gain	0.9900
6:30562383:TCACA:T	acceptor_loss	0.9900
6:30562384:CACAG:C	acceptor_loss	0.9900
6:30562385:ACAG:A	acceptor_loss	0.9900
6:30562386:CA:C	acceptor_loss	0.9900
6:30562387:A:AG	acceptor_gain	0.9900
6:30562387:AG:A	acceptor_loss	0.9900
6:30562388:G:GG	acceptor_gain	0.9900
6:30562388:GAC:G	acceptor_gain	0.9900
6:30562388:GACA:G	acceptor_gain	0.9900
6:30562388:GACAA:G	acceptor_gain	0.9900
6:30562388:GA:G	acceptor_gain	0.9800
6:30557447:ATCGG:A	donor_loss	0.9700
6:30557449:CGGT:C	donor_loss	0.9700
6:30557450:GGT:G	donor_loss	0.9700
6:30557451:GTGA:G	donor_loss	0.9700
6:30557452:T:C	donor_loss	0.9700
6:30561832:A:AG	acceptor_gain	0.9700
6:30561833:G:GG	acceptor_gain	0.9700
6:30557451:G:GG	donor_gain	0.9600
6:30561567:A:T	donor_gain	0.9600

AlphaMissense

1208 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:30562460:T:C	F178L	0.999
6:30562462:C:A	F178L	0.999
6:30562462:C:G	F178L	0.999
6:30562436:T:A	C170S	0.998
6:30562437:G:C	C170S	0.998
6:30562454:T:A	C176S	0.998
6:30562455:G:C	C176S	0.998
6:30562409:T:A	C161S	0.997
6:30562409:T:C	C161R	0.997
6:30562410:G:C	C161S	0.997
6:30562418:T:C	F164L	0.997
6:30562420:T:A	F164L	0.997
6:30562420:T:G	F164L	0.997
6:30562454:T:C	C176R	0.997
6:30562455:G:A	C176Y	0.997
6:30562436:T:C	C170R	0.996
6:30562437:G:A	C170Y	0.996
6:30562410:G:A	C161Y	0.995
6:30562438:T:G	C170W	0.995
6:30562466:C:G	H180D	0.995
6:30562468:T:A	H180Q	0.995
6:30562468:T:G	H180Q	0.995
6:30562411:C:G	C161W	0.994
6:30562455:G:T	C176F	0.994
6:30562456:T:G	C176W	0.994
6:30562437:G:T	C170F	0.993
6:30562461:T:C	F178S	0.993
6:30562417:T:A	H163Q	0.991
6:30562417:T:G	H163Q	0.991
6:30562461:T:G	F178C	0.991

dbSNP variants (sampled 300 via entrez): RS1000220560 (6:30560701 T>C,G), RS1001070829 (6:30559742 A>G), RS1001235962 (6:30559153 G>A), RS1001394831 (6:30558297 A>G), RS1002665586 (6:30558601 G>A,T), RS1003068344 (6:30562900 CTTGTT>C), RS1003253338 (6:30560023 G>T), RS1003475422 (6:30557932 A>G), RS1003852173 (6:30559984 G>A), RS1004132247 (6:30559603 A>T), RS1005261712 (6:30560422 C>T), RS1005642343 (6:30557494 C>T), RS1005856461 (6:30558833 C>A), RS1005943606 (6:30557093 AATT>A), RS1006977142 (6:30564183 GA>G)

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

19 associations (top):

Study	Trait	p-value
GCST004521_114	Autism spectrum disorder or schizophrenia	3.000000e-17
GCST004521_117	Autism spectrum disorder or schizophrenia	3.000000e-15
GCST004521_121	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_132	Autism spectrum disorder or schizophrenia	2.000000e-09
GCST004521_171	Autism spectrum disorder or schizophrenia	4.000000e-14
GCST004521_2	Autism spectrum disorder or schizophrenia	2.000000e-16
GCST004521_209	Autism spectrum disorder or schizophrenia	5.000000e-16
GCST004521_210	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_211	Autism spectrum disorder or schizophrenia	5.000000e-15
GCST004521_263	Autism spectrum disorder or schizophrenia	7.000000e-17
GCST004521_265	Autism spectrum disorder or schizophrenia	7.000000e-14
GCST004521_269	Autism spectrum disorder or schizophrenia	7.000000e-11
GCST004521_295	Autism spectrum disorder or schizophrenia	6.000000e-18
GCST004521_3	Autism spectrum disorder or schizophrenia	2.000000e-15
GCST004521_56	Autism spectrum disorder or schizophrenia	1.000000e-22
GCST004521_70	Autism spectrum disorder or schizophrenia	8.000000e-20
GCST004521_79	Autism spectrum disorder or schizophrenia	1.000000e-16
GCST004861_76	Itch intensity from mosquito bite	2.000000e-08
GCST005232_23	Neuroticism	8.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008377	mosquito bite reaction itch intensity measurement
EFO:0007660	neuroticism measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

32 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, affects cotreatment, increases abundance, increases expression	2
dicrotophos	increases expression	1
pirinixic acid	increases activity, increases expression, affects binding	1
quercitrin	decreases expression	1
beta-lapachone	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
beta-methylcholine	affects expression	1
cylindrospermopsin	increases expression	1
Resveratrol	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Arsenic Trioxide	increases response to substance	1
Air Pollutants	affects expression, increases abundance	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	decreases expression	1
Calcitriol	decreases expression, affects cotreatment	1
Diazinon	increases methylation	1
Doxorubicin	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methotrexate	decreases expression	1
Ozone	affects expression, increases abundance	1
Plant Extracts	affects cotreatment, increases expression	1
Silicon Dioxide	decreases expression	1
Testosterone	decreases expression, affects cotreatment	1
Thiram	decreases expression	1
Tretinoin	decreases expression	1
Urethane	decreases expression	1
Vincristine	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	affects expression	1
Asbestos, Crocidolite	decreases expression	1

Clinical trials (associated diseases)

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