PRR15L

Summary

PRR15L (proline rich 15 like, HGNC:28149) is a protein-coding gene on chromosome 17q21.32, encoding Proline-rich protein 15-like protein (Q9BU68).

At a glance

• GWAS associations: 5
• Clinical variants (ClinVar): 28 total
• MANE Select transcript: NM_024320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28149
Approved symbol	PRR15L
Name	proline rich 15 like
Location	17q21.32
Locus type	gene with protein product
Status	Approved
Aliases	MGC11242
Ensembl gene	ENSG00000167183
Ensembl biotype	protein_coding
Entrez	79170

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 12 protein_coding

ENST00000300557, ENST00000902772, ENST00000902773, ENST00000902774, ENST00000902775, ENST00000902776, ENST00000902777, ENST00000902778, ENST00000902779, ENST00000902780, ENST00000963507, ENST00000963508

RefSeq mRNA: 1 — MANE Select: NM_024320 NM_024320

CCDS: CCDS11523

Canonical transcript exons

ENST00000300557 — 2 exons

Exon	Start	End
ENSE00001110691	47957657	47957883
ENSE00001110692	47951967	47953263

Expression profiles

Bgee: expression breadth ubiquitous, 184 present calls, max score 98.28.

FANTOM5 (CAGE): breadth broad, TPM avg 12.4179 / max 511.2158, expressed in 334 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
166619	11.7010	331
166618	0.7169	141

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
ileal mucosa	UBERON:0000331	98.28	gold quality
mucosa of transverse colon	UBERON:0004991	98.05	gold quality
rectum	UBERON:0001052	97.85	gold quality
duodenum	UBERON:0002114	96.68	gold quality
body of pancreas	UBERON:0001150	96.60	gold quality
jejunal mucosa	UBERON:0000399	95.82	gold quality
pancreatic ductal cell	CL:0002079	94.76	gold quality
left lobe of thyroid gland	UBERON:0001120	93.74	gold quality
colonic mucosa	UBERON:0000317	93.49	gold quality
right lobe of thyroid gland	UBERON:0001119	93.35	gold quality
thyroid gland	UBERON:0002046	92.96	gold quality
mucosa of sigmoid colon	UBERON:0004993	92.62	gold quality
pancreas	UBERON:0001264	92.26	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	91.85	gold quality
parotid gland	UBERON:0001831	91.29	gold quality
minor salivary gland	UBERON:0001830	90.78	gold quality
saliva-secreting gland	UBERON:0001044	90.53	gold quality
small intestine	UBERON:0002108	89.30	gold quality
small intestine Peyer’s patch	UBERON:0003454	89.21	gold quality
transverse colon	UBERON:0001157	88.93	gold quality
nasal cavity epithelium	UBERON:0005384	88.07	gold quality
metanephros cortex	UBERON:0010533	87.25	gold quality
gall bladder	UBERON:0002110	87.06	gold quality
mouth mucosa	UBERON:0003729	87.01	gold quality
lower esophagus mucosa	UBERON:0035834	86.79	gold quality
islet of Langerhans	UBERON:0000006	86.77	gold quality
upper lobe of left lung	UBERON:0008952	86.37	gold quality
adult mammalian kidney	UBERON:0000082	86.33	gold quality
body of stomach	UBERON:0001161	86.16	gold quality
upper lobe of lung	UBERON:0008948	86.01	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	17.37
E-GEOD-125970	yes	6.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

63 targeting PRR15L, 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-3689D	100.00	66.14	1181
HSA-MIR-6851-5P	100.00	65.63	1294
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-15A-5P	99.90	72.80	2787
HSA-MIR-15B-5P	99.90	72.78	2798
HSA-MIR-16-5P	99.90	72.80	2780
HSA-MIR-195-5P	99.90	72.81	2805
HSA-MIR-424-5P	99.89	71.90	2641
HSA-MIR-6838-5P	99.89	71.94	2690
HSA-MIR-3065-3P	99.87	70.25	1407
HSA-MIR-1299	99.77	71.24	2389
HSA-MIR-132-3P	99.73	70.56	1424
HSA-MIR-212-3P	99.73	70.65	1424
HSA-MIR-6752-3P	99.72	66.71	1587
HSA-MIR-4530	99.69	66.47	1509
HSA-MIR-6832-5P	99.58	64.82	1132
HSA-MIR-190A-5P	99.54	71.45	933
HSA-MIR-190B-5P	99.54	71.40	925
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4696	99.48	67.48	1040
HSA-MIR-6081	99.48	66.07	1446
HSA-MIR-302A-5P	99.39	68.21	1913
HSA-MIR-4722-3P	99.35	65.22	1099
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Prr15l	ENSMUSG00000047040
rattus_norvegicus	Prr15l	ENSRNOG00000049162

Paralogs (1): PRR15 (ENSG00000176532)

Protein

Protein identifiers

Proline-rich protein 15-like protein — Q9BU68 (reviewed: Q9BU68)

Alternative names: Protein ATAD4

All UniProt accessions (2): A0A140VJT1, Q9BU68

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the PRR15 family.

RefSeq proteins (1): NP_077296* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028237	PRR15	Family

Pfam: PF15321

UniProt features (4 total): compositionally biased region 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BU68-F1	64.08	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 80 (showing top): GOZGIT_ESR1_TARGETS_DN, WEI_MYCN_TARGETS_WITH_E_BOX, CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP, CAIRO_HEPATOBLASTOMA_UP, NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON, MODULE_342, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, MASSARWEH_TAMOXIFEN_RESISTANCE_UP, MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MODULE_139, MIKKELSEN_MEF_LCP_WITH_H3K27ME3

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

1022 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRR15L	PNPO	Q9NVS9	545
PRR15L	ZNF706	Q9Y5V0	508
PRR15L	PRR15	Q8IV56	506
PRR15L	ZNF888	P0CJ79	501
PRR15L	ASB8	Q9H765	479
PRR15L	OSBPL7	Q9BZF2	474
PRR15L	NFE2L1	Q14494	458
PRR15L	PLLP	Q9Y342	443
PRR15L	C1orf116	Q9BW04	427
PRR15L	C9orf152	Q5JTZ5	415
PRR15L	CCDC9	Q9Y3X0	412
PRR15L	CCDC184	Q52MB2	409
PRR15L	SMIM5	Q71RC9	400
PRR15L	DALRD3	Q5D0E6	397
PRR15L	ZNF593	O00488	374

IntAct

0 interactions, top by confidence:

BioGRID (1): PRR15L (Proximity Label-MS)

ESM2 similar proteins: B9DGG8, F4HV65, F4I5N6, F4J424, O22611, P53604, P93017, P98190, Q05349, Q0WL69, Q10060, Q10296, Q1G3K8, Q1PF35, Q32NP7, Q3KR53, Q3T183, Q3ZBW7, Q52KW0, Q566Z6, Q5F368, Q5HZ09, Q5R3Z9, Q5R787, Q5R9C3, Q5U2R6, Q5XII9, Q63HQ0, Q6DBU1, Q6GLU8, Q6NZP2, Q6PD31, Q7T3E8, Q7XPT0, Q8BQS4, Q8JZM2, Q8S307, Q8WWR9, Q94CK6, Q9BU68

Diamond homologs: Q3T183, Q566Z6, Q6DBU1, Q8JZM2, Q9BU68, Q8IV56, Q9D1T5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

416 predictions. Top by Δscore:

Variant	Effect	Δscore
17:47953264:CTG:C	acceptor_gain	0.9900
17:47953267:C:CC	acceptor_gain	0.9900
17:47953273:C:CT	acceptor_gain	0.9900
17:47953274:A:T	acceptor_gain	0.9900
17:47953277:G:C	acceptor_gain	0.9800
17:47953277:G:GC	acceptor_gain	0.9800
17:47953265:TG:T	acceptor_gain	0.9700
17:47953267:CT:C	acceptor_loss	0.9700
17:47953268:T:A	acceptor_loss	0.9700
17:47953262:TTCTG:T	acceptor_gain	0.9600
17:47954671:A:C	acceptor_gain	0.9600
17:47953260:CTTT:C	acceptor_gain	0.9500
17:47953262:TTC:T	acceptor_loss	0.9400
17:47953263:TCT:T	acceptor_loss	0.9400
17:47953264:C:CG	acceptor_loss	0.9400
17:47953265:T:A	acceptor_loss	0.9400
17:47957651:CTGTA:C	donor_loss	0.9400
17:47957652:TGTA:T	donor_loss	0.9400
17:47957653:GTAC:G	donor_loss	0.9400
17:47957654:TACCT:T	donor_loss	0.9400
17:47957655:A:AC	donor_loss	0.9400
17:47957656:C:CC	donor_loss	0.9400
17:47957695:T:A	donor_gain	0.9400
17:47953261:TTT:T	acceptor_gain	0.9300
17:47953269:G:C	acceptor_loss	0.9300
17:47957473:G:C	donor_gain	0.9300
17:47957657:C:A	donor_loss	0.9300
17:47953266:G:C	acceptor_loss	0.9000
17:47953259:GCTTT:G	acceptor_gain	0.8800
17:47953260:CTTTC:C	acceptor_gain	0.8800

AlphaMissense

667 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
17:47953004:C:A	K77N	0.998
17:47953004:C:G	K77N	0.998
17:47953007:G:C	F76L	0.998
17:47953007:G:T	F76L	0.998
17:47953009:A:G	F76L	0.998
17:47953012:G:T	R75S	0.998
17:47953014:C:T	G74E	0.998
17:47953008:A:G	F76S	0.997
17:47953032:A:T	V68D	0.997
17:47953014:C:A	G74V	0.995
17:47953006:T:C	K77E	0.994
17:47953011:C:G	R75P	0.994
17:47953023:G:A	S71F	0.994
17:47953024:A:G	S71P	0.994
17:47953026:A:T	V70D	0.994
17:47953199:G:C	F12L	0.994
17:47953199:G:T	F12L	0.994
17:47953201:A:G	F12L	0.994
17:47953008:A:C	F76C	0.992
17:47953015:C:G	G74R	0.991
17:47953015:C:T	G74R	0.991
17:47953018:A:G	S73P	0.991
17:47953012:G:C	R75G	0.990
17:47952986:T:A	R83S	0.988
17:47952986:T:G	R83S	0.988
17:47953023:G:T	S71Y	0.987
17:47953026:A:G	V70A	0.987
17:47953009:A:C	F76V	0.986
17:47953005:T:A	K77M	0.985
17:47953005:T:G	K77T	0.985

dbSNP variants (sampled 300 via entrez): RS1000034933 (17:47953069 C>T), RS1001259171 (17:47952473 G>T), RS1001388726 (17:47953673 AAAGAAG>A,AAAG,AAAGAAGAAG,AAAGAAGAAGAAG), RS1001419651 (17:47954018 C>T), RS1002172849 (17:47958466 C>T), RS1002843972 (17:47955366 C>T), RS1003177220 (17:47956796 G>A), RS1003589785 (17:47959455 G>A), RS1003695702 (17:47952456 C>T), RS1003709710 (17:47957104 A>T), RS1004068541 (17:47959661 A>G), RS1004933834 (17:47953311 G>A), RS1005162501 (17:47959767 A>G), RS1005169080 (17:47955349 G>T), RS1005541431 (17:47959436 G>A)

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

5 associations (top):

Study	Trait	p-value
GCST001662_4	Generalized epilepsy	9.000000e-09
GCST005951_17	Body mass index	3.000000e-09
GCST90013445_11	Type 1 diabetes	3.000000e-09
GCST90013445_71	Type 1 diabetes	3.000000e-09
GCST90014023_6	Type 1 diabetes	1.000000e-09

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	decreases methylation, affects methylation, decreases expression	4
Estradiol	increases expression, decreases expression, affects cotreatment	4
Aflatoxin B1	decreases expression, decreases methylation, increases methylation	4
Nickel	decreases expression	2
Valproic Acid	affects expression, decreases expression, increases methylation	2
3,19-(2-bromobenzylidene)andrographolide	decreases response to substance, increases expression	1
bisphenol F	affects cotreatment, increases methylation	1
pirinixic acid	decreases expression, increases activity, affects binding	1
bisphenol A	decreases expression	1
lead acetate	decreases expression	1
beta-lapachone	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
cupric chloride	decreases expression	1
gallium arsenide	decreases expression	1
pentanal	decreases expression	1
CGP 52608	affects binding, increases reaction	1
abrine	decreases expression	1
ormosil	affects binding, decreases expression	1
bisphenol S	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Leflunomide	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Cisplatin	increases expression	1
Dichlorodiphenyl Dichloroethylene	decreases expression	1
Dimethyl Sulfoxide	increases expression	1
Hydrogen Peroxide	affects expression	1

Clinical trials (associated diseases)

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