PLP2

gene
On this page

Also known as A4A4-LSBMGC126187

Summary

PLP2 (proteolipid protein 2, HGNC:9087) is a protein-coding gene on chromosome Xp11.23, encoding Proteolipid protein 2 (Q04941). May play a role in cell differentiation in the intestinal epithelium.

This gene encodes an integral membrane protein that localizes to the endoplasmic reticulum in colonic epithelial cells. The encoded protein can multimerize and may function as an ion channel. A polymorphism in the promoter of this gene may be linked to an increased risk of X-linked cognitive disability. A pseudogene of this gene is found on chromosome 5.

Source: NCBI Gene 5355 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 46 total
  • Druggable target: yes
  • MANE Select transcript: NM_002668

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9087
Approved symbolPLP2
Nameproteolipid protein 2
LocationXp11.23
Locus typegene with protein product
StatusApproved
AliasesA4, A4-LSB, MGC126187
Ensembl geneENSG00000102007
Ensembl biotypeprotein_coding
OMIM300112
Entrez5355

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000376322, ENST00000376327, ENST00000879549, ENST00000935268

RefSeq mRNA: 1 — MANE Select: NM_002668 NM_002668

CCDS: CCDS14319

Canonical transcript exons

ENST00000376327 — 5 exons

ExonStartEnd
ENSE000006702654917433549174425
ENSE000006702674917338849173483
ENSE000006702694917312949173281
ENSE000014702034917467249175235
ENSE000038510184917189849172096

Expression profiles

Bgee: expression breadth ubiquitous, 267 present calls, max score 99.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 190.9998 / max 3605.2796, expressed in 1788 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
196320114.53591777
19631939.84781717
19632136.61611681

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gingival epitheliumUBERON:000194999.43gold quality
gingivaUBERON:000182899.35gold quality
skin of abdomenUBERON:000141699.24gold quality
descending thoracic aortaUBERON:000234599.20gold quality
esophagus mucosaUBERON:000246999.17gold quality
skin of legUBERON:000151199.16gold quality
right coronary arteryUBERON:000162599.13gold quality
thoracic aortaUBERON:000151599.10gold quality
ascending aortaUBERON:000149699.09gold quality
zone of skinUBERON:000001499.08gold quality
aortaUBERON:000094799.05gold quality
nippleUBERON:000203099.05gold quality
popliteal arteryUBERON:000225099.04gold quality
tibial arteryUBERON:000761099.04gold quality
upper leg skinUBERON:000426299.03gold quality
body of pancreasUBERON:000115099.00gold quality
tongue squamous epitheliumUBERON:000691998.98gold quality
lower esophagus mucosaUBERON:003583498.97gold quality
pharyngeal mucosaUBERON:000035598.96gold quality
penisUBERON:000098998.95gold quality
vaginaUBERON:000099698.92gold quality
mammalian vulvaUBERON:000099798.92gold quality
esophagusUBERON:000104398.91gold quality
skin of hipUBERON:000155498.88gold quality
left coronary arteryUBERON:000162698.87gold quality
mucosa of stomachUBERON:000119998.80gold quality
left adrenal gland cortexUBERON:003582598.78gold quality
monocyteCL:000057698.76gold quality
left adrenal glandUBERON:000123498.76gold quality
right adrenal glandUBERON:000123398.72gold quality

Single-cell (SCXA)

Detected in 23 experiment(s), a significant marker in 19.

ExperimentMarker?Max mean expression
E-MTAB-7407yes589.97
E-CURD-112yes465.65
E-MTAB-6701yes89.92
E-CURD-114yes72.29
E-HCAD-4yes67.75
E-HCAD-6yes62.05
E-GEOD-125970yes24.91
E-MTAB-10042yes16.56
E-MTAB-9467yes16.38
E-HCAD-10yes15.30
E-MTAB-9067yes15.21
E-MTAB-8498yes13.38
E-CURD-122yes13.32
E-CURD-46yes10.15
E-GEOD-135922yes9.98

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

38 targeting PLP2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-150-5P99.9966.691976
HSA-MIR-548AN99.9770.912817
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-552-5P99.9368.561583
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-76599.8468.242442
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-6892-3P99.6866.401178
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-7-5P99.6770.531809
HSA-MIR-452799.6667.43714
HSA-MIR-715099.6266.801322
HSA-MIR-6503-5P99.6266.96597
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-1212399.5271.792990
HSA-MIR-642A-5P99.5165.101152
HSA-MIR-3678-3P99.3167.101432
HSA-MIR-1273H-3P99.2967.55980
HSA-MIR-3692-5P99.2967.041421
HSA-MIR-5582-5P99.2771.421879
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-4777-3P99.1568.92626
HSA-MIR-6768-3P99.1467.381319
HSA-MIR-465199.0667.572002
HSA-MIR-316499.0268.391071
HSA-MIR-6820-3P99.0268.501035
HSA-MIR-184398.9766.07838

Literature-anchored findings (GeneRIF, showing 16)

  • PLP2/A4 has a role in the chemotactic processes via CCR1 (PMID:15474493)
  • PLP2 is expressed abundantly in the pyramidal cells of hippocampus and granular cells of the cerebellum in the brains of a cohort of males with probable X-linked mental retardation. (PMID:17416750)
  • This work ascribes a critical function to PLP2 for viral ligase activity and underlines the power of non-lethal haploid genetic screens in human cells to identify the genes involved in pathogen manipulation of the host immune system. (PMID:24278019)
  • PLP2 and RAB5C are binding partners of TPD52. (PMID:24604726)
  • PLP2 specifically binds to phosphatidylinositol 3 kinase to activate the protein kinase B pathway to enhance cell proliferation, adhesion, and invasion in melanoma cells. (PMID:26287415)
  • Up-regulation of miR-422a attenuated microsphere formation, proliferation and tumor formation of breast cancer stem cells via suppressing the PLP2 expression. (PMID:29509055)
  • Higher PLP2 immunohistochemistry staining significantly correlated with more advanced tumor grades and poorer prognosis in human gliomas. (PMID:30373180)
  • Reduced expression of proteolipid protein 2 increases ER stress-induced apoptosis and autophagy in glioblastoma. (PMID:31778016)
  • MiR-765 functions as a tumour suppressor and eliminates lipids in clear cell renal cell carcinoma by downregulating PLP2. (PMID:31901870)
  • PLP2 Expression as a Prognostic and Therapeutic Indicator in High-Risk Multiple Myeloma. (PMID:32596309)
  • CD45RO(-)CD8(+) T cell-derived exosomes restrict estrogen-driven endometrial cancer development via the ERbeta/miR-765/PLP2/Notch axis. (PMID:33859750)
  • PLP2 drives collective cell migration via ZO-1-mediated cytoskeletal remodeling at the leading edge in human colorectal cancer cells. (PMID:34409455)
  • PLP2-derived peptide Rb4 triggers PARP-1-mediated necrotic death in murine melanoma cells. (PMID:35190586)
  • Structural basis of plp2-mediated cytoskeletal protein folding by TRiC/CCT. (PMID:36921056)
  • Low Expression of A3C and PLP2 Indicating a Favorable Prognosis in Human Gliomas. (PMID:37715423)
  • Reduced Proteolipid Protein 2 promotes endoplasmic reticulum stress-related apoptosis and increases drug sensitivity in acute myeloid leukemia. (PMID:38085372)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_rerioplp2bENSDARG00000036630
danio_rerioplp2aENSDARG00000042972
mus_musculusPlp2ENSMUSG00000031146
mus_musculusPlp2rtENSMUSG00000057762
rattus_norvegicusPlp2ENSRNOG00000039496
rattus_norvegicusPlp2l1ENSRNOG00000055728
caenorhabditis_elegansF28H1.4WBGENE00017909
caenorhabditis_elegansF47B3.3WBGENE00018527

Paralogs (14): CMTM1 (ENSG00000089505), CMTM6 (ENSG00000091317), PLLP (ENSG00000102934), CMTM3 (ENSG00000140931), CMTM2 (ENSG00000140932), MALL (ENSG00000144063), MAL2 (ENSG00000147676), CMTM7 (ENSG00000153551), MARVELD1 (ENSG00000155254), CMTM5 (ENSG00000166091), CMTM8 (ENSG00000170293), MAL (ENSG00000172005), CMTM4 (ENSG00000183723), CKLF (ENSG00000217555)

Protein

Protein identifiers

Proteolipid protein 2Q04941 (reviewed: Q04941)

Alternative names: Differentiation-dependent protein A4, Intestinal membrane A4 protein

All UniProt accessions (1): Q04941

UniProt curated annotations — full annotation on UniProt →

Function. May play a role in cell differentiation in the intestinal epithelium.

Subcellular location. Membrane.

Tissue specificity. Enriched in colonic mucosa. The expression of A4 follows a gradient along the crypto-villus axis with the most abundant message occurring in the lower half of the crypt.

Isoforms (2)

UniProt IDNamesCanonical?
Q04941-11yes
Q04941-22

RefSeq proteins (1): NP_002659* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008253MarvelDomain
IPR050578MARVEL-CKLF_proteinsFamily

Pfam: PF01284

UniProt features (10 total): transmembrane region 4, glycosylation site 2, chain 1, domain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q04941-F178.760.22

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Glycosylation sites (2): 18, 108

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 314 (showing top): RNGTGGGC_UNKNOWN, RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP, HORIUCHI_WTAP_TARGETS_DN, GOBP_RESPONSE_TO_PEPTIDE, XU_GH1_AUTOCRINE_TARGETS_UP, JAEGER_METASTASIS_DN, MODULE_151, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, HSIAO_HOUSEKEEPING_GENES, GGGTGGRR_PAX4_03, AAAYRNCTG_UNKNOWN, TTGGGAG_MIR150

GO Biological Process (4): monoatomic ion transport (GO:0006811), chemotaxis (GO:0006935), cytokine-mediated signaling pathway (GO:0019221), monoatomic ion transmembrane transport (GO:0034220)

GO Molecular Function (3): monoatomic ion transmembrane transporter activity (GO:0015075), chemokine binding (GO:0019956), protein binding (GO:0005515)

GO Cellular Component (4): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
transport1
response to chemical1
taxis1
cell surface receptor signaling pathway1
cellular response to cytokine stimulus1
monoatomic ion transport1
transmembrane transport1
transmembrane transporter activity1
monoatomic ion transmembrane transport1
cytokine binding1
binding1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

738 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PLP2PLP1P04400995
PLP2PDCL2Q8N4E4894
PLP2PDCL3Q9H2J4840
PLP2BECN1Q14457774
PLP2IRF3Q14653701
PLP2TUBB2AQ13885649
PLP2TUBBP05218642
PLP2TCP1P17987588
PLP2SH2D3CQ8N5H7572
PLP2ZUP1Q96AP4553
PLP2PPP1CAP08129547
PLP2PDCP20941532
PLP2SH2D3AQ9BRG2479
PLP2ISG15P05161476
PLP2USP2O75604444

IntAct

227 interactions, top by confidence:

ABTypeScore
TMEM79PLP2psi-mi:“MI:0915”(physical association)0.670
PLP2TMEM79psi-mi:“MI:0915”(physical association)0.670
TMPRSS2PLP2psi-mi:“MI:0915”(physical association)0.600
PLP2KASH5psi-mi:“MI:0915”(physical association)0.560
KASH5PLP2psi-mi:“MI:0915”(physical association)0.560
PLP2HSD17B13psi-mi:“MI:0915”(physical association)0.560
PLP2TMEM51psi-mi:“MI:0915”(physical association)0.560
PLP2CYB561psi-mi:“MI:0915”(physical association)0.560
PLP2SCN3Bpsi-mi:“MI:0915”(physical association)0.560
PLP2ELOVL5psi-mi:“MI:0915”(physical association)0.560
PLP2LHFPL5psi-mi:“MI:0915”(physical association)0.560
PLP2psi-mi:“MI:0915”(physical association)0.560
ARFIP2PLP2psi-mi:“MI:0915”(physical association)0.560
PLP2FATE1psi-mi:“MI:0915”(physical association)0.560
HSBP1L1PLP2psi-mi:“MI:0915”(physical association)0.560
PLP2RNF5psi-mi:“MI:0915”(physical association)0.560
PLP2SLC14A2psi-mi:“MI:0915”(physical association)0.560
ASGR2PLP2psi-mi:“MI:0915”(physical association)0.560
PLP2BNIP3psi-mi:“MI:0915”(physical association)0.560
PLP2BIKpsi-mi:“MI:0915”(physical association)0.560
PLP2PACC1psi-mi:“MI:0915”(physical association)0.560

BioGRID (120): TMEM79 (Two-hybrid), CCDC155 (Two-hybrid), PLP2 (Affinity Capture-MS), PLP2 (Affinity Capture-MS), PLP2 (Proximity Label-MS), PLP2 (Affinity Capture-MS), PLP2 (Affinity Capture-MS), PLP2 (Affinity Capture-RNA), PLP2 (Two-hybrid), PLP2 (Two-hybrid), PLP2 (Affinity Capture-MS), PLP2 (Synthetic Lethality), PLP2 (Two-hybrid), PLP2 (Two-hybrid), PLP2 (Two-hybrid)

ESM2 similar proteins: A2VE13, A4K2N5, A4K2W1, B8BPI2, E1BY51, O09117, O09198, O35682, O62646, O88662, O89104, P21145, Q04941, Q10EJ2, Q16563, Q1RMQ3, Q28296, Q3URJ8, Q3ZBY0, Q5R6H1, Q5RAI2, Q5VXT5, Q64349, Q6DHB5, Q6GPN9, Q6P0C6, Q6P742, Q6VBQ5, Q6Y1E2, Q78S06, Q86TG1, Q86UW1, Q8BI08, Q8CJ61, Q8IZ96, Q8IZR5, Q8N2H4, Q8N8D7, Q91WN2, Q95MN6

Diamond homologs: Q04941, Q28597, Q6P742, Q6Y1E2, Q95MN6, Q96DZ9, Q99LJ5, Q9D6G9, Q9R1Q7, Q96MX0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance17
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (0)

SpliceAI

811 predictions. Top by Δscore:

VariantEffectΔscore
X:49172074:G:Tdonor_gain1.0000
X:49172093:GATT:Gdonor_gain1.0000
X:49172097:G:GGdonor_gain1.0000
X:49173277:GGAGT:Gdonor_gain1.0000
X:49173278:GAGT:Gdonor_gain1.0000
X:49173278:GAGTG:Gdonor_gain1.0000
X:49173280:GT:Gdonor_gain1.0000
X:49173282:G:GGdonor_gain1.0000
X:49173380:C:Gacceptor_gain1.0000
X:49173383:CACA:Cacceptor_loss1.0000
X:49173385:CA:Cacceptor_loss1.0000
X:49173386:A:ATacceptor_loss1.0000
X:49173387:G:Cacceptor_loss1.0000
X:49173481:GGG:Gdonor_gain1.0000
X:49173482:GGG:Gdonor_gain1.0000
X:49173523:GGTT:Gdonor_gain1.0000
X:49173668:G:Tdonor_gain1.0000
X:49174325:T:Aacceptor_gain1.0000
X:49174329:CCCCA:Cacceptor_loss1.0000
X:49174330:CCCA:Cacceptor_loss1.0000
X:49174331:CCAGG:Cacceptor_loss1.0000
X:49174332:CAGGT:Cacceptor_loss1.0000
X:49174333:A:Cacceptor_loss1.0000
X:49174333:AG:Aacceptor_gain1.0000
X:49174334:GG:Gacceptor_gain1.0000
X:49174422:ACTGG:Adonor_loss1.0000
X:49174426:G:GGdonor_gain1.0000
X:49172073:G:GTdonor_gain0.9900
X:49172095:TT:Tdonor_gain0.9900
X:49173125:CCA:Cacceptor_loss0.9900

AlphaMissense

974 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
X:49174341:G:CG118R0.984
X:49172073:G:AG25R0.983
X:49172073:G:CG25R0.983
X:49173270:T:AW80R0.983
X:49173270:T:CW80R0.983
X:49173410:C:AA91E0.983
X:49173135:T:CC35R0.981
X:49173398:G:CR87P0.977
X:49173279:A:CS83R0.974
X:49173281:T:AS83R0.974
X:49173281:T:GS83R0.974
X:49173137:C:GC35W0.972
X:49174342:G:AG118D0.972
X:49174365:G:CG126R0.972
X:49173481:G:AG115R0.968
X:49173481:G:CG115R0.968
X:49174366:G:AG126D0.968
X:49173482:G:AG115E0.965
X:49173156:T:CF42L0.962
X:49173158:C:AF42L0.962
X:49173158:C:GF42L0.962
X:49173272:G:CW80C0.962
X:49173272:G:TW80C0.962
X:49174375:C:AA129D0.960
X:49172074:G:AG25E0.958
X:49174356:T:CC123R0.958
X:49172083:T:CL28P0.957
X:49172093:G:CE31D0.956
X:49172093:G:TE31D0.956
X:49173136:G:AC35Y0.956

dbSNP variants (sampled 300 via entrez): RS1000441232 (X:49172441 G>A), RS1000822608 (X:49174266 C>A), RS1001940945 (X:49173716 G>A,C), RS1004391357 (X:49171018 C>T), RS1004675270 (X:49173571 G>A,T), RS1004726216 (X:49173171 C>A,T), RS1006399805 (X:49175392 G>A), RS1008198471 (X:49170449 C>T), RS1011837805 (X:49169933 C>G), RS1013098987 (X:49172001 A>C,G), RS1013157305 (X:49171397 C>G,T), RS1013440986 (X:49174217 G>A), RS1014759412 (X:49173616 G>C), RS1014863204 (X:49172648 G>T), RS1016540890 (X:49174926 A>G)

Disease associations

OMIM: gene MIM:300112 | 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):

StudyTraitp-value
GCST90002401_287Platelet distribution width9.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067398 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression, affects expression, decreases expression9
Cadmium Chlorideincreases palmitoylation, decreases expression, increases expression, decreases reaction, increases abundance3
bisphenol Aaffects cotreatment, decreases methylation, decreases expression2
entinostataffects cotreatment, increases expression2
Benzo(a)pyreneaffects methylation, increases expression, increases methylation2
Cadmiumdecreases expression, decreases reaction, increases abundance, increases palmitoylation2
Doxorubicinaffects expression, decreases expression2
Tretinoindecreases expression2
aristolochic acid Idecreases expression1
dicrotophosincreases expression1
triphenyl phosphateaffects expression1
salinomycindecreases expression1
beta-lapachoneincreases expression1
methylparabenincreases expression1
sodium arseniteincreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
cadmium acetatedecreases expression1
di-n-butylphosphoric acidaffects expression1
CD 437decreases expression1
deguelinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
dorsomorphinaffects cotreatment, increases expression1
jinfukangincreases expression1
(+)-JQ1 compounddecreases expression1
Resveratrolincreases expression1
Temozolomidedecreases expression1
Decitabineincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Acetaminophendecreases expression1
Atrazinedecreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5652069BindingBinding affinity to human PLP2 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Cellosaurus cell lines

2 cell lines: 2 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_TE70HAP1 PLP2 (-) 1Cancer cell lineMale
CVCL_TE71HAP1 PLP2 (-) 2Cancer cell lineMale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.