PACRGL

Summary

PACRGL (parkin coregulated like, HGNC:28442) is a protein-coding gene on chromosome 4p15.31, encoding PACRG-like protein (Q8N7B6).

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_001258345

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28442
Approved symbol	PACRGL
Name	parkin coregulated like
Location	4p15.31
Locus type	gene with protein product
Status	Approved
Aliases	MGC29898
Ensembl gene	ENSG00000163138
Ensembl biotype	protein_coding
Entrez	133015

Gene structure

Transcript identifiers

Ensembl transcripts: 83 — 74 protein_coding, 6 nonsense_mediated_decay, 2 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000295290, ENST00000360916, ENST00000444671, ENST00000467997, ENST00000471979, ENST00000502374, ENST00000502938, ENST00000503585, ENST00000503747, ENST00000504630, ENST00000505160, ENST00000506457, ENST00000506552, ENST00000506648, ENST00000506702, ENST00000506745, ENST00000506951, ENST00000507634, ENST00000508753, ENST00000508952, ENST00000509469, ENST00000509625, ENST00000510051, ENST00000510700, ENST00000511089, ENST00000511160, ENST00000513459, ENST00000513590, ENST00000513861, ENST00000514292, ENST00000514485, ENST00000514663, ENST00000515339, ENST00000886677, ENST00000886678, ENST00000886679, ENST00000886680, ENST00000886681, ENST00000886682, ENST00000886683, ENST00000886684, ENST00000886685, ENST00000886686, ENST00000886687, ENST00000886688, ENST00000886689, ENST00000886690, ENST00000886691, ENST00000886692, ENST00000886693, ENST00000886694, ENST00000886695, ENST00000886696, ENST00000886697, ENST00000886698, ENST00000886699, ENST00000886700, ENST00000886701, ENST00000886702, ENST00000933230, ENST00000933231, ENST00000933232, ENST00000933233, ENST00000933234, ENST00000933235, ENST00000933236, ENST00000969731, ENST00000969732, ENST00000969733, ENST00000969734, ENST00000969735, ENST00000969736, ENST00000969737, ENST00000969738, ENST00000969739, ENST00000969740, ENST00000969741, ENST00000969742, ENST00000969743, ENST00000969744, ENST00000969745, ENST00000969746, ENST00000969747

RefSeq mRNA: 9 — MANE Select: NM_001258345 NM_001130727, NM_001258345, NM_001258346, NM_001317849, NM_001330745, NM_001330746, NM_001330747, NM_001330748, NM_145048

CCDS: CCDS3427, CCDS47034, CCDS58895, CCDS58896, CCDS82912

Canonical transcript exons

ENST00000503585 — 9 exons

Exon	Start	End
ENSE00001071973	20704660	20704814
ENSE00002049188	20700458	20700787
ENSE00002078389	20727285	20732557
ENSE00003505180	20712788	20712922
ENSE00003597069	20724808	20724888
ENSE00003599177	20709683	20709773
ENSE00003608111	20713432	20713539
ENSE00003643219	20704466	20704533
ENSE00003785827	20707803	20707870

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 98.24.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.4343 / max 100.3925, expressed in 1796 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47074	11.3739	1791
47073	1.0605	695

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	98.24	gold quality
left testis	UBERON:0004533	93.96	gold quality
right testis	UBERON:0004534	93.82	gold quality
buccal mucosa cell	CL:0002336	92.51	gold quality
testis	UBERON:0000473	92.37	gold quality
calcaneal tendon	UBERON:0003701	92.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	92.06	gold quality
right uterine tube	UBERON:0001302	88.93	gold quality
tendon	UBERON:0000043	88.48	gold quality
ventricular zone	UBERON:0003053	88.32	gold quality
right ovary	UBERON:0002118	86.97	gold quality
left ovary	UBERON:0002119	86.78	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	86.74	gold quality
body of uterus	UBERON:0009853	86.51	gold quality
left lobe of thyroid gland	UBERON:0001120	86.46	gold quality
tibial nerve	UBERON:0001323	86.23	gold quality
oviduct epithelium	UBERON:0004804	86.10	gold quality
right lobe of thyroid gland	UBERON:0001119	86.01	gold quality
thyroid gland	UBERON:0002046	85.82	gold quality
Brodmann (1909) area 9	UBERON:0013540	85.75	gold quality
ganglionic eminence	UBERON:0004023	85.48	gold quality
cortical plate	UBERON:0005343	85.42	gold quality
adenohypophysis	UBERON:0002196	85.35	gold quality
muscle layer of sigmoid colon	UBERON:0035805	85.31	gold quality
smooth muscle tissue	UBERON:0001135	85.30	gold quality
prefrontal cortex	UBERON:0000451	85.20	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	85.06	gold quality
endocervix	UBERON:0000458	84.99	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.69	gold quality
rectum	UBERON:0001052	84.67	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

57 targeting PACRGL, 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-3163	100.00	77.23	8605
HSA-MIR-196A-5P	100.00	68.16	684
HSA-MIR-196B-5P	100.00	68.16	681
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-3143	99.93	71.96	3104
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-548AZ-5P	99.83	69.94	3230
HSA-MIR-548T-5P	99.83	69.91	3220
HSA-MIR-636	99.80	69.58	1500
HSA-MIR-187-5P	99.74	70.26	1404
HSA-MIR-4719	99.73	72.10	3329
HSA-MIR-4699-3P	99.71	70.15	3142
HSA-MIR-4470	99.66	69.35	1767
HSA-MIR-7844-5P	99.55	68.56	1428
HSA-MIR-6733-3P	99.54	67.80	1281
HSA-MIR-143-3P	99.49	69.05	1457
HSA-MIR-4770	99.49	69.09	1451
HSA-MIR-6507-5P	99.36	70.46	2524
HSA-MIR-130A-5P	99.33	70.26	2623

Literature-anchored findings (GeneRIF, showing 1)

• Exosomal circPACRGL promotes progression of colorectal cancer via the miR-142-3p/miR-506-3p- TGF-beta1 axis. (PMID:32713345)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	5730480H06Rik	ENSMUSG00000029089
rattus_norvegicus	Pacrgl	ENSRNOG00000004140

Paralogs (1): PACRG (ENSG00000112530)

Protein

Protein identifiers

PACRG-like protein — Q8N7B6 (reviewed: Q8N7B6)

All UniProt accessions (20): Q8N7B6, D6R9D1, D6R9F1, D6R9N9, D6RA69, D6RAL7, D6RAM4, D6RB63, D6RBZ2, D6RC13, D6RC23, D6RD40, D6RDH3, D6REJ6, D6REQ4, D6RF08, D6RF51, D6RF67, D6RGK2, H0YA87

Isoforms (4)

UniProt ID	Names	Canonical?
Q8N7B6-1	1	yes
Q8N7B6-2	2
Q8N7B6-3	3
Q8N7B6-4	4

RefSeq proteins (9): NP_001124199, NP_001245274, NP_001245275, NP_001304778, NP_001317674, NP_001317675, NP_001317676, NP_001317677, NP_659485 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR011989	ARM-like	Homologous_superfamily
IPR016024	ARM-type_fold	Homologous_superfamily
IPR019399	Parkin_co-regulated_protein	Family

Pfam: PF10274

UniProt features (11 total): splice variant 4, compositionally biased region 2, modified residue 2, chain 1, region of interest 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7B6-F1	78.64	0.64

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 (2): 1, 47

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 82 (showing top): GSE45365_NK_CELL_VS_BCELL_UP, ATF_B, ATF3_Q6, LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN, CHEN_ETV5_TARGETS_TESTIS, CREBP1CJUN_01, CREB_01, SANSOM_APC_TARGETS, TGACGTCA_ATF3_Q6, chr4p15, KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN, FIGUEROA_AML_METHYLATION_CLUSTER_3_UP, JOHNSTONE_PARVB_TARGETS_3_DN, BRUINS_UVC_RESPONSE_LATE, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

1788 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PACRGL	MEIG1	Q5JSS6	564
PACRGL	FAM184B	Q9ULE4	524
PACRGL	SHKBP1	Q8TBC3	487
PACRGL	TEFM	Q96QE5	481
PACRGL	ADGRA3	Q8IWK6	475
PACRGL	AFG1L	Q8WV93	434
PACRGL	SLIT2	O94813	414
PACRGL	KCNIP4	Q6PIL6	409
PACRGL	XYLB	O75191	398
PACRGL	ENKUR	Q8TC29	392
PACRGL	DHX15	O43143	387
PACRGL	ANKRD42	Q8N9B4	373
PACRGL	SLIT3	O75094	342
PACRGL	ZNF609	O15014	339
PACRGL	FBXO33	Q7Z6M2	310

IntAct

12 interactions, top by confidence:

A	B	Type	Score
MYOG	PACRGL	psi-mi:“MI:0915”(physical association)	0.560
RCN3	PACRGL	psi-mi:“MI:0915”(physical association)	0.560
PACRGL	MYOG	psi-mi:“MI:0915”(physical association)	0.560
PACRGL	RCN3	psi-mi:“MI:0915”(physical association)	0.560
RPN1	APBB1	psi-mi:“MI:0914”(association)	0.530
PACRGL	FAM3A	psi-mi:“MI:0915”(physical association)	0.370
DDOST	ATL3	psi-mi:“MI:0914”(association)	0.350
OST4	ATL3	psi-mi:“MI:0914”(association)	0.350
RPN2	APBB1	psi-mi:“MI:0914”(association)	0.350

BioGRID (20): PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), GOLGA2 (Two-hybrid), ALX1 (Two-hybrid), BEX5 (Two-hybrid), ZBTB10 (Two-hybrid), TXNRD3 (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Two-hybrid), PACRGL (Positive Genetic)

ESM2 similar proteins: A0A3Q1LSX9, A1A5G0, A1A5K2, A2A5R2, A2APV2, A2VE70, D3ZYR1, O00203, O04376, O35643, O60308, O75122, P52303, Q05397, Q08AM6, Q08DS7, Q0JRZ9, Q10567, Q13367, Q28FH2, Q32PG1, Q3UQN2, Q4U0G1, Q561M0, Q5R807, Q5ZIW5, Q6NUP7, Q6NXC0, Q6NYW6, Q6ZPF4, Q7TSU1, Q7YRF1, Q7Z460, Q80TV8, Q8BRT1, Q8C0Y0, Q8IVF7, Q8LF36, Q8N7B6, Q8RW96

Diamond homologs: Q8N7B6, Q9D3X5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	25
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2546 predictions. Top by Δscore:

Variant	Effect	Δscore
4:20704656:CCAG:C	acceptor_loss	1.0000
4:20704658:A:AG	acceptor_gain	1.0000
4:20704659:G:A	acceptor_loss	1.0000
4:20704659:G:GA	acceptor_gain	1.0000
4:20704659:GGT:G	acceptor_gain	1.0000
4:20704659:GGTA:G	acceptor_gain	1.0000
4:20704659:GGTAA:G	acceptor_gain	1.0000
4:20704786:A:AG	donor_gain	1.0000
4:20704815:G:GA	donor_loss	1.0000
4:20704815:G:GG	donor_gain	1.0000
4:20704816:T:G	donor_loss	1.0000
4:20707801:A:AG	acceptor_gain	1.0000
4:20707802:G:GG	acceptor_gain	1.0000
4:20707855:G:GT	donor_gain	1.0000
4:20711536:A:T	donor_gain	1.0000
4:20713395:T:A	acceptor_gain	1.0000
4:20713535:CAAGC:C	donor_gain	1.0000
4:20713536:AAGC:A	donor_gain	1.0000
4:20713537:AGC:A	donor_gain	1.0000
4:20713538:GC:G	donor_gain	1.0000
4:20713538:GCG:G	donor_gain	1.0000
4:20713538:GCGT:G	donor_loss	1.0000
4:20713539:CG:C	donor_loss	1.0000
4:20713540:G:GA	donor_loss	1.0000
4:20713540:G:GG	donor_gain	1.0000
4:20713541:T:TC	donor_loss	1.0000
4:20724792:A:AG	acceptor_gain	1.0000
4:20731999:TAC:T	donor_loss	1.0000
4:20732000:ACTT:A	donor_loss	1.0000
4:20732001:CT:C	donor_loss	1.0000

AlphaMissense

1588 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:20709717:T:A	W104R	0.999
4:20709717:T:C	W104R	0.999
4:20709719:G:C	W104C	0.999
4:20709719:G:T	W104C	0.999
4:20707866:T:C	C91R	0.998
4:20709712:T:C	L102S	0.997
4:20712788:G:C	G123R	0.997
4:20727321:T:G	Y243D	0.997
4:20709685:T:C	L93S	0.996
4:20709718:G:C	W104S	0.996
4:20724869:T:C	L224P	0.996
4:20712792:T:C	L124P	0.995
4:20712822:T:A	V134E	0.995
4:20712833:G:C	G138R	0.995
4:20713484:T:C	L185P	0.995
4:20713486:A:C	S186R	0.995
4:20713488:T:A	S186R	0.995
4:20713488:T:G	S186R	0.995
4:20709690:C:G	H95D	0.994
4:20707834:T:C	F80S	0.993
4:20707845:T:G	Y84D	0.993
4:20709769:C:A	A121D	0.993
4:20712789:G:A	G123D	0.993
4:20712809:C:T	P130S	0.993
4:20712810:C:A	P130Q	0.993
4:20712834:G:A	G138D	0.993
4:20713520:T:C	L197P	0.993
4:20707868:C:G	C91W	0.992
4:20709768:G:C	A121P	0.992
4:20713475:T:C	L182P	0.992

dbSNP variants (sampled 300 via entrez): RS1000013014 (4:20715059 T>G), RS1000030016 (4:20738937 T>G), RS1000057601 (4:20733288 C>T), RS1000076809 (4:20723160 A>C), RS1000123750 (4:20765912 A>T), RS1000231471 (4:20716631 G>C,T), RS1000254109 (4:20760000 A>G), RS1000286376 (4:20727468 T>C), RS10003206 (4:20741787 G>A,C,T), RS1000407385 (4:20720960 A>G), RS1000408962 (4:20760141 G>C), RS1000474458 (4:20766137 G>A,C), RS1000547825 (4:20700577 C>T), RS1000566781 (4:20729199 T>C), RS1000592414 (4:20707163 A>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

2 associations (top):

Study	Trait	p-value
GCST005648_39	Serum metabolite concentrations in chronic kidney disease	9.000000e-10
GCST009391_558	Metabolite levels	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0009769	histidine measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
FR900359	affects phosphorylation	1
butyraldehyde	decreases expression	1
pentanal	decreases expression	1
pentabromodiphenyl ether	increases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	increases expression	1
Sunitinib	increases expression	1
Ethinyl Estradiol	increases expression	1
Gallic Acid	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Mitoxantrone	affects response to substance	1
Silicon Dioxide	increases expression	1
Tretinoin	decreases expression	1
Valproic Acid	decreases expression	1
Zinc	increases expression	1
Cyclosporine	increases expression	1
Cadmium Chloride	decreases expression	1
Copper Sulfate	decreases expression	1

Clinical trials (associated diseases)

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