PRMT2IP

Summary

PRMT2IP (PRMT2 interacting protein, HGNC:24497) is a protein-coding gene on chromosome 15q24.2, encoding Uncharacterized protein C15orf39 (Q6ZRI6). Negatively regulates microglial inflammatory responses.

Located in cytosol.

Source: NCBI Gene 56905 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 32 total
• MANE Select transcript: NM_015492

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:24497
Approved symbol	PRMT2IP
Name	PRMT2 interacting protein
Location	15q24.2
Locus type	gene with protein product
Status	Approved
Aliases	DKFZP434H132, FLJ46337
Ensembl gene	ENSG00000167173
Ensembl biotype	protein_coding
OMIM	621142
Entrez	56905

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 10 protein_coding

ENST00000360639, ENST00000394987, ENST00000562637, ENST00000563905, ENST00000564848, ENST00000565074, ENST00000567617, ENST00000899650, ENST00000899651, ENST00000899652

RefSeq mRNA: 1 — MANE Select: NM_015492 NM_015492

CCDS: CCDS10276

Canonical transcript exons

ENST00000394987 — 3 exons

Exon	Start	End
ENSE00001431512	75205999	75208824
ENSE00001520243	75201882	75202059
ENSE00003536645	75210749	75212169

Expression profiles

Bgee: expression breadth ubiquitous, 224 present calls, max score 95.14.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 40.6216 / max 1838.3931, expressed in 1809 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147785	36.0714	1806
147786	1.0917	246
147788	0.8148	372
147793	0.7530	371
147784	0.4740	73
147796	0.3995	176
147791	0.2658	91
147794	0.2055	46
147787	0.1656	62
147790	0.1621	66

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	95.14	gold quality
right testis	UBERON:0004534	94.75	gold quality
monocyte	CL:0000576	94.37	gold quality
leukocyte	CL:0000738	94.34	gold quality
mononuclear cell	CL:0000842	94.31	gold quality
granulocyte	CL:0000094	93.43	gold quality
testis	UBERON:0000473	92.68	gold quality
blood	UBERON:0000178	92.24	gold quality
popliteal artery	UBERON:0002250	89.26	gold quality
tibial artery	UBERON:0007610	89.25	gold quality
right coronary artery	UBERON:0001625	86.57	gold quality
bone marrow cell	CL:0002092	86.45	gold quality
aorta	UBERON:0000947	86.43	gold quality
spleen	UBERON:0002106	85.73	gold quality
mucosa of transverse colon	UBERON:0004991	84.81	gold quality
apex of heart	UBERON:0002098	84.72	gold quality
lower esophagus mucosa	UBERON:0035834	84.71	gold quality
right ovary	UBERON:0002118	84.61	gold quality
esophagus mucosa	UBERON:0002469	84.61	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	84.55	gold quality
left coronary artery	UBERON:0001626	84.49	gold quality
buccal mucosa cell	CL:0002336	84.43	gold quality
left ovary	UBERON:0002119	84.23	gold quality
left uterine tube	UBERON:0001303	84.11	gold quality
upper lobe of left lung	UBERON:0008952	83.94	gold quality
coronary artery	UBERON:0001621	83.77	gold quality
right adrenal gland	UBERON:0001233	83.62	gold quality
left adrenal gland	UBERON:0001234	83.46	gold quality
right uterine tube	UBERON:0001302	83.45	gold quality
left adrenal gland cortex	UBERON:0035825	83.42	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	7.89
E-MTAB-6075	no	137.90

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting PRMT2IP, 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-4692	100.00	67.32	2066
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-MIR-98-5P	99.98	72.33	1787
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-1197	99.70	67.75	1027
HSA-MIR-4441	99.49	66.56	3216
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-125A-5P	99.36	70.59	1640
HSA-MIR-125B-5P	99.36	70.36	1662
HSA-MIR-4641	99.28	66.64	744

Literature-anchored findings (GeneRIF, showing 1)

• Human C15orf39 Inhibits Inflammatory Response via PRMT2 in Human Microglial HMC3 Cell Line. (PMID:38892217)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	1700017B05Rik	ENSMUSG00000032300
rattus_norvegicus	C8h15orf39	ENSRNOG00000018689

Protein

Protein identifiers

Uncharacterized protein C15orf39 — Q6ZRI6 (reviewed: Q6ZRI6)

All UniProt accessions (5): H3BMJ2, H3BN41, H3BRS2, H3BT66, Q6ZRI6

UniProt curated annotations — full annotation on UniProt →

Function. Negatively regulates microglial inflammatory responses. Inhibits NF-kappa-B signaling by interacting with PRMT2, thereby reducing the production of pro-inflammatory cytokines, maintaining a steady-state in microglia and limiting excessive inflammation.

Subunit / interactions. Interacts with PRMT2.

Subcellular location. Cytoplasm. Nucleus.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6ZRI6-1	1	yes
Q6ZRI6-2	2
Q6ZRI6-3	3

RefSeq proteins (1): NP_056307* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR037656	DUF5525	Family

Pfam: PF17663

UniProt features (37 total): modified residue 12, region of interest 9, compositionally biased region 5, splice variant 4, sequence variant 4, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZRI6-F1	49.18	0.11

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 (12): 17, 208, 299, 391, 397, 455, 496, 497, 936, 956, 988, 996

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 192 (showing top): LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP, GOBP_INFLAMMATORY_RESPONSE, GOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION, GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION, RICKMAN_METASTASIS_DN, AP1_Q4_01, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, GOBP_REGULATION_OF_RESPONSE_TO_STRESS, GOBP_NEGATIVE_REGULATION_OF_DEFENSE_RESPONSE, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN, GOBP_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE, TGANTCA_AP1_C, GOBP_NEGATIVE_REGULATION_OF_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION

GO Biological Process (2): negative regulation of canonical NF-kappaB signal transduction (GO:0043124), negative regulation of inflammatory response (GO:0050728)

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

GO Cellular Component (3): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
canonical NF-kappaB signal transduction	1
regulation of canonical NF-kappaB signal transduction	1
negative regulation of intracellular signal transduction	1
inflammatory response	1
negative regulation of defense response	1
negative regulation of response to external stimulus	1
regulation of inflammatory response	1
binding	1
intracellular membrane-bounded organelle	1
intracellular anatomical structure	1
cytoplasm	1

Protein interactions and networks

STRING

456 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PRMT2IP	FAM219B	Q5XKK7	581
PRMT2IP	UBL7	Q96S82	479
PRMT2IP	C19orf47	Q8N9M1	447
PRMT2IP	GPALPP1	Q8IXQ4	434
PRMT2IP	ULK3	Q6PHR2	400
PRMT2IP	SCAMP5	Q8TAC9	400
PRMT2IP	FAM193B	Q96PV7	400
PRMT2IP	CSTPP1	Q9H6J7	373
PRMT2IP	RSRP1	Q9BUV0	370
PRMT2IP	LMAN1L	Q9HAT1	370
PRMT2IP	ZNF606	Q8WXB4	370
PRMT2IP	GOLGA6A	Q9NYA3	368
PRMT2IP	ARSF	P54793	350
PRMT2IP	C9J5N1	C9J5N1	349
PRMT2IP	PLEKHG3	A1L390	348
PRMT2IP	MOB3A	Q96BX8	348

IntAct

53 interactions, top by confidence:

A	B	Type	Score
MAD2L1BP	LBR	psi-mi:“MI:0914”(association)	0.730
CTBP1	CBX4	psi-mi:“MI:0914”(association)	0.700
MAD2L1	INSR	psi-mi:“MI:0914”(association)	0.700
CCNJL	PIK3C2A	psi-mi:“MI:0914”(association)	0.530
BAG2	HGS	psi-mi:“MI:0914”(association)	0.530
MAD2L1BP	KIF20A	psi-mi:“MI:0914”(association)	0.530
MAD2L1	PPIP5K2	psi-mi:“MI:0914”(association)	0.530
C15orf39	CTBP2	psi-mi:“MI:0915”(physical association)	0.370
HSP90B1	DERL1	psi-mi:“MI:0914”(association)	0.350
Xpo1	IFT56	psi-mi:“MI:0914”(association)	0.350
rep	SBNO1	psi-mi:“MI:0914”(association)	0.350
CAPZB	ENAH	psi-mi:“MI:0914”(association)	0.350
hspa1a_hspa1b_human-1	SHTN1	psi-mi:“MI:0914”(association)	0.350
CDC16	IFT56	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT2	IFT56	psi-mi:“MI:0914”(association)	0.350
PPP4R1L	IFT56	psi-mi:“MI:0914”(association)	0.350
MAD2L1	MED19	psi-mi:“MI:0914”(association)	0.350
S100A2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
RFPL4B	KRBA1	psi-mi:“MI:0914”(association)	0.350
PRMT2	KRBA1	psi-mi:“MI:0914”(association)	0.350
SCPEP1	CCDC85C	psi-mi:“MI:0914”(association)	0.350
OLFM2	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
NCAPH2	MYO9A	psi-mi:“MI:0914”(association)	0.350
ZNG1B	NME4	psi-mi:“MI:0914”(association)	0.350
UMODL1	C2CD2L	psi-mi:“MI:0914”(association)	0.350
RAD51B	APAF1	psi-mi:“MI:0914”(association)	0.350
AOPEP	ZBTB39	psi-mi:“MI:0914”(association)	0.350
AFG3L2	TBX3	psi-mi:“MI:0914”(association)	0.350
CRYAA	TRIM24	psi-mi:“MI:0914”(association)	0.350
CARD8	HDAC3	psi-mi:“MI:0914”(association)	0.350

BioGRID (104): C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Proximity Label-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS), C15orf39 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUS0, A0A5F9ZHS7, A7E346, A7MB34, A8MZG2, B2RU40, D4A9R4, O08574, O75593, P0C1Z6, P0CG20, Q0VG99, Q0ZCJ7, Q17QH7, Q29RM2, Q2KIS6, Q2M2S6, Q2M3G4, Q2NL68, Q32LE6, Q3U1J1, Q5JXC2, Q5R815, Q5SW24, Q61660, Q63247, Q6NZ36, Q6PBC9, Q6ZN01, Q6ZRI6, Q7TN08, Q7Z591, Q80VF6, Q86WR7, Q8BG26, Q8BP99, Q8BXQ8, Q8IYS4, Q8N9Y4, Q8NAV2

Diamond homologs: Q3TEI4, Q6ZRI6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

721 predictions. Top by Δscore:

Variant	Effect	Δscore
15:75205995:CCAG:C	acceptor_loss	0.9900
15:75205997:A:C	acceptor_loss	0.9900
15:75205998:G:GA	acceptor_loss	0.9900
15:75210743:TTCCA:T	acceptor_loss	0.9900
15:75210744:TCCA:T	acceptor_loss	0.9900
15:75210745:CCA:C	acceptor_loss	0.9900
15:75210746:CA:C	acceptor_loss	0.9900
15:75210747:A:C	acceptor_loss	0.9900
15:75210747:AGGT:A	acceptor_gain	0.9900
15:75210748:GGT:G	acceptor_gain	0.9900
15:75210748:GGTG:G	acceptor_gain	0.9900
15:75205997:A:AG	acceptor_gain	0.9800
15:75205998:G:GG	acceptor_gain	0.9800
15:75208820:GCTGG:G	donor_gain	0.9800
15:75209613:C:G	donor_gain	0.9800
15:75209627:A:AG	donor_gain	0.9800
15:75210747:A:AG	acceptor_gain	0.9800
15:75210748:G:GG	acceptor_gain	0.9800
15:75210748:GGTGA:G	acceptor_gain	0.9800
15:75204019:TGG:T	donor_gain	0.9700
15:75209665:C:A	donor_gain	0.9700
15:75199120:A:G	donor_gain	0.9600
15:75199136:C:G	donor_gain	0.9600
15:75202055:TGCAG:T	donor_loss	0.9600
15:75202057:CAGG:C	donor_loss	0.9600
15:75202058:AG:A	donor_loss	0.9600
15:75202059:GGT:G	donor_loss	0.9600
15:75202060:G:GA	donor_loss	0.9600
15:75202061:T:A	donor_loss	0.9600
15:75208821:C:G	donor_gain	0.9600

AlphaMissense

6626 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:75207567:T:C	F507L	0.999
15:75207568:T:C	F507S	0.999
15:75207569:C:A	F507L	0.999
15:75207569:C:G	F507L	0.999
15:75207570:A:C	S508R	0.999
15:75207572:C:A	S508R	0.999
15:75207572:C:G	S508R	0.999
15:75208575:T:C	F843L	0.999
15:75208577:C:A	F843L	0.999
15:75208577:C:G	F843L	0.999
15:75208598:G:C	K850N	0.999
15:75208598:G:T	K850N	0.999
15:75208576:T:C	F843S	0.998
15:75208742:G:C	K898N	0.998
15:75208742:G:T	K898N	0.998
15:75208744:T:C	L899S	0.998
15:75208576:T:G	F843C	0.997
15:75208582:C:A	P845H	0.997
15:75208666:T:C	L873P	0.997
15:75208687:A:T	E880V	0.997
15:75208545:T:C	F833L	0.996
15:75208546:T:C	F833S	0.996
15:75208547:C:A	F833L	0.996
15:75208547:C:G	F833L	0.996
15:75208582:C:G	P845R	0.996
15:75208608:T:C	F854L	0.996
15:75208609:T:C	F854S	0.996
15:75208610:C:A	F854L	0.996
15:75208610:C:G	F854L	0.996
15:75208688:G:C	E880D	0.996

dbSNP variants (sampled 300 via entrez): RS1000312733 (15:75198707 C>A,T), RS1000428732 (15:75198950 C>T), RS1000487914 (15:75211934 G>A), RS1000505129 (15:75200446 A>C,T), RS1000532700 (15:75200004 C>A,G), RS1000660131 (15:75197123 C>G), RS1000868442 (15:75203365 C>T), RS1000978321 (15:75203676 G>T), RS1001019520 (15:75209622 T>C,G), RS1001135082 (15:75210027 T>C,G), RS1001489860 (15:75210709 G>A,T), RS1001652648 (15:75204763 G>A), RS1001991001 (15:75203097 G>T), RS1002107193 (15:75203252 G>A), RS1002173676 (15:75208927 A>G,T)

Disease associations

OMIM: gene MIM:621142 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST004749_41	Lung cancer in ever smokers	6.000000e-06
GCST90002396_639	Mean reticulocyte volume	2.000000e-18
GCST90002397_264	Mean spheric corpuscular volume	3.000000e-12

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases methylation, increases expression	3
bisphenol A	decreases methylation, increases expression	2
Acetaminophen	increases expression	2
Cisplatin	affects cotreatment, increases expression, decreases expression	2
Aflatoxin B1	increases methylation	2
Cadmium Chloride	decreases expression, increases expression	2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
FR900359	decreases phosphorylation	1
bisphenol F	affects cotreatment, decreases expression	1
TAK-243	increases sumoylation	1
dicrotophos	increases expression	1
triphenyl phosphate	affects expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	increases expression	1
ochratoxin A	decreases expression	1
benzo(e)pyrene	increases methylation	1
potassium chromate(VI)	increases expression, affects cotreatment	1
ferrous chloride	decreases expression	1
aflatoxin B2	increases methylation	1
epigallocatechin gallate	increases expression, affects cotreatment	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
bisphenol S	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
PCI 5002	affects cotreatment, increases expression	1
Arsenic	affects methylation	1
Hexachlorocyclohexane	decreases expression	1
Caffeine	affects phosphorylation	1
Copper	affects binding, decreases expression	1

Clinical trials (associated diseases)

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