PRR9

Summary

PRR9 (proline rich 9, HGNC:32057) is a protein-coding gene on chromosome 1q21.3, encoding Proline-rich protein 9 (Q5T870).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 16 total
• MANE Select transcript: NM_001195571

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:32057
Approved symbol	PRR9
Name	proline rich 9
Location	1q21.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000203783
Ensembl biotype	protein_coding
Entrez	574414

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000368744

RefSeq mRNA: 1 — MANE Select: NM_001195571 NM_001195571

CCDS: CCDS55639

Canonical transcript exons

ENST00000368744 — 2 exons

Exon	Start	End
ENSE00001447887	153218125	153219310
ENSE00001447888	153217584	153217619

Expression profiles

Bgee: expression breadth broad, 86 present calls, max score 97.28.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7758 / max 237.7166, expressed in 59 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
5380	0.7758	59

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	97.28	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	94.13	silver quality
sperm	CL:0000019	93.55	gold quality
skin of hip	UBERON:0001554	83.51	gold quality
germinal epithelium of ovary	UBERON:0001304	69.09	gold quality
nipple	UBERON:0002030	64.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.03	gold quality
ileal mucosa	UBERON:0000331	61.39	silver quality
zone of skin	UBERON:0000014	60.67	gold quality
right testis	UBERON:0004534	59.68	gold quality
left testis	UBERON:0004533	59.58	gold quality
amniotic fluid	UBERON:0000173	59.18	silver quality
skin of abdomen	UBERON:0001416	58.80	gold quality
deltoid	UBERON:0001476	58.42	silver quality
cardiac muscle of right atrium	UBERON:0003379	58.07	silver quality
pancreatic ductal cell	CL:0002079	58.02	silver quality
testis	UBERON:0000473	57.83	gold quality
skin of leg	UBERON:0001511	57.79	gold quality
endothelial cell	CL:0000115	56.17	gold quality
parietal pleura	UBERON:0002400	55.06	silver quality
visceral pleura	UBERON:0002401	54.69	gold quality
epithelial cell of pancreas	CL:0000083	54.41	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
bone marrow cell	CL:0002092	53.31	silver quality
tonsil	UBERON:0002372	51.09	gold quality
gingiva	UBERON:0001828	48.71	silver quality
gingival epithelium	UBERON:0001949	48.19	silver quality
quadriceps femoris	UBERON:0001377	47.85	gold quality
tongue	UBERON:0001723	47.49	silver quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-3929	yes	188.50
E-ANND-3	no	0.81

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): ELF3

miRNA regulators (miRDB)

54 targeting PRR9, 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-3924	100.00	72.09	2394
HSA-MIR-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
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-8068	99.98	73.85	2376
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-146A-5P	99.96	68.93	988
HSA-MIR-146B-5P	99.96	69.13	977
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-7153-5P	99.94	68.89	1006
HSA-MIR-4778-3P	99.93	70.40	1818
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-MIR-4492	99.87	68.25	3611
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4766-5P	99.75	69.23	2662
HSA-MIR-3685	99.62	68.83	1621
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-3612	99.45	66.02	1333
HSA-MIR-650	99.45	65.77	1309
HSA-MIR-6507-3P	99.35	67.32	1059
HSA-MIR-520F-5P	99.34	70.40	1632
HSA-MIR-6128	99.33	67.83	1581
HSA-MIR-146A-3P	99.13	68.99	1881
HSA-MIR-6809-5P	99.13	68.45	1223

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prr9	ENSMUSG00000056270
rattus_norvegicus	Prr9	ENSRNOG00000012312

Paralogs (20): LCE2B (ENSG00000159455), SPRR2G (ENSG00000159516), LCE3D (ENSG00000163202), SPRR3 (ENSG00000163209), SPRR1B (ENSG00000169469), SPRR1A (ENSG00000169474), LCE1D (ENSG00000172155), SPRR4 (ENSG00000184148), LCE3A (ENSG00000185962), LCE3E (ENSG00000185966), LCE5A (ENSG00000186207), LCE1E (ENSG00000186226), LCE2A (ENSG00000187173), LCE2C (ENSG00000187180), LCE2D (ENSG00000187223), LCE3B (ENSG00000187238), KPLCE (ENSG00000198854), LELP1 (ENSG00000203784), LCE1F (ENSG00000240386), LCE3C (ENSG00000244057)

Protein

Protein identifiers

Proline-rich protein 9 — Q5T870 (reviewed: Q5T870)

All UniProt accessions (1): Q5T870

RefSeq proteins (1): NP_001182500* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR052888	PRR9	Family

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5T870-F1	49.42	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN, SENESE_HDAC1_TARGETS_UP, RICKMAN_HEAD_AND_NECK_CANCER_C, chr1q21, SENESE_HDAC1_AND_HDAC2_TARGETS_UP, MARTENS_TRETINOIN_RESPONSE_UP, MIR4766_5P, MIR146A_3P, MIR122B_5P, MIR1304_5P, MIR876_3P, MIR212_5P, MIR6804_5P, MIR3188, MIR323A_5P

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

396 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR9	PRR7	Q8TB68	871
PRR9	TRNT1	Q96Q11	795
PRR9	PRR5	P85299	665
PRR9	ELF4	Q99607	642
PRR9	LELP1	Q5T871	574
PRR9	RNF215	Q9Y6U7	544
PRR9	ELF3	P78545	511
PRR9	KPLCE	Q5T750	491
PRR9	VSIG8	P0DPA2	480
PRR9	KPRP	Q5T749	470
PRR9	CRCT1	Q9UGL9	452
PRR9	HDAC6	Q9UBN7	433
PRR9	SPRR4	Q96PI1	432
PRR9	ILDR1	Q86SU0	400
PRR9	LCE3A	Q5TA76	396

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTR4, A6QNZ4, O14633, O70554, O70555, O70556, O70557, O70558, O70559, O70560, O70562, P15265, P22528, P22531, P22532, P35321, P35322, P35323, P35324, P35325, P35326, P49901, Q28658, Q32L04, Q4KL71, Q4R956, Q5T5B0, Q5T750, Q5T752, Q5T754, Q5T870, Q5T871, Q5TA76, Q5TA77, Q5TA78, Q5TA79, Q5TA81, Q5TA82, Q5TCM9, Q62266

Diamond homologs: A6QNZ4, Q5T870, Q8BV84

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	14
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

53 predictions. Top by Δscore:

Variant	Effect	Δscore
1:153218123:A:AG	acceptor_gain	0.9700
1:153218124:G:GG	acceptor_gain	0.9700
1:153217618:AGG:A	donor_loss	0.9600
1:153217621:T:A	donor_loss	0.9400
1:153218121:TCAG:T	acceptor_loss	0.9300
1:153218122:CAGG:C	acceptor_loss	0.9300
1:153218123:A:AC	acceptor_loss	0.9300
1:153218123:AG:A	acceptor_gain	0.9300
1:153218124:GG:G	acceptor_gain	0.9300
1:153218124:GGCT:G	acceptor_gain	0.9200
1:153217620:G:GG	donor_gain	0.9100
1:153217616:TCAG:T	donor_gain	0.8500
1:153217617:CAG:C	donor_gain	0.8300
1:153217618:AG:A	donor_gain	0.8300
1:153217619:GG:G	donor_gain	0.8300
1:153217615:ATCAG:A	donor_gain	0.8200
1:153218124:GGC:G	acceptor_gain	0.7300
1:153218124:GGCTC:G	acceptor_gain	0.7300
1:153218121:TCAGG:T	acceptor_gain	0.6700
1:153218122:CAGGC:C	acceptor_gain	0.6700
1:153218107:ATCTT:A	acceptor_loss	0.5900
1:153217620:G:T	donor_gain	0.5500
1:153218113:T:TA	acceptor_gain	0.5200
1:153217599:T:G	donor_gain	0.5000
1:153218123:AGGC:A	acceptor_gain	0.4500
1:153218111:T:A	acceptor_gain	0.4400
1:153218120:TTCAG:T	acceptor_gain	0.4400
1:153218108:T:G	acceptor_loss	0.3900
1:153218125:G:T	acceptor_loss	0.3800
1:153218124:G:T	acceptor_gain	0.3700

AlphaMissense

759 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:153218151:T:C	F3L	0.926
1:153218153:C:A	F3L	0.926
1:153218153:C:G	F3L	0.926
1:153218180:T:G	C12W	0.766
1:153218178:T:C	C12R	0.747
1:153218152:T:G	F3C	0.711
1:153218152:T:C	F3S	0.688
1:153218492:G:C	K116N	0.686
1:153218492:G:T	K116N	0.686
1:153218193:T:C	C17R	0.652
1:153218195:C:G	C17W	0.649
1:153218243:C:G	C33W	0.603
1:153218491:A:C	K116T	0.601
1:153218179:G:A	C12Y	0.594

dbSNP variants (sampled 300 via entrez): RS1002216499 (1:153216548 A>G), RS1002540427 (1:153217781 G>T), RS1002611589 (1:153216236 A>G), RS1002960471 (1:153217961 A>G), RS1003550572 (1:153217393 C>G,T), RS1004001073 (1:153218109 C>A), RS1004012347 (1:153218397 T>A,C), RS1005687251 (1:153219787 C>G,T), RS1006503894 (1:153219344 C>A), RS1007395087 (1:153217735 T>C), RS1009016296 (1:153216635 G>A), RS1009029253 (1:153217021 C>A,T), RS1009579637 (1:153215870 A>G), RS1009633731 (1:153216158 A>G), RS1010864106 (1:153216752 T>C)

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

1 associations (top):

Study	Trait	p-value
GCST008916_87	Asthma	2.000000e-13

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2
ethyl-p-hydroxybenzoate	decreases expression	1
hydroquinone	increases expression	1
gallium arsenide	increases expression	1
Sodium Dodecyl Sulfate	increases expression	1
Asbestos, Crocidolite	affects expression	1
Cadmium Chloride	increases expression	1
Particulate Matter	increases expression	1

Clinical trials (associated diseases)

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