ERGIC2

gene
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Also known as PTX1Erv41

Summary

ERGIC2 (ERGIC and golgi 2, HGNC:30208) is a protein-coding gene on chromosome 12p11.22, encoding Endoplasmic reticulum-Golgi intermediate compartment protein 2 (Q96RQ1). Possible role in transport between endoplasmic reticulum and Golgi.

ERGIC2, or PTX1, is a ubiquitously expressed nuclear protein that is downregulated in prostate carcinoma (Kwok et al., 2001 [PubMed 11445006]).

Source: NCBI Gene 51290 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 69 total — 1 pathogenic
  • MANE Select transcript: NM_016570

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:30208
Approved symbolERGIC2
NameERGIC and golgi 2
Location12p11.22
Locus typegene with protein product
StatusApproved
AliasesPTX1, Erv41
Ensembl geneENSG00000087502
Ensembl biotypeprotein_coding
OMIM612236
Entrez51290

Gene structure

Transcript identifiers

Ensembl transcripts: 23 — 20 protein_coding, 2 nonsense_mediated_decay, 1 retained_intron

ENST00000360150, ENST00000546509, ENST00000546839, ENST00000548098, ENST00000548441, ENST00000548909, ENST00000549182, ENST00000550353, ENST00000551467, ENST00000552132, ENST00000552155, ENST00000869902, ENST00000869903, ENST00000869904, ENST00000869905, ENST00000869906, ENST00000869907, ENST00000869908, ENST00000869909, ENST00000869910, ENST00000869911, ENST00000966762, ENST00000966763

RefSeq mRNA: 1 — MANE Select: NM_016570 NM_016570

CCDS: CCDS41765

Canonical transcript exons

ENST00000360150 — 14 exons

ExonStartEnd
ENSE000005573442935001329350068
ENSE000005573452934907929349177
ENSE000007343822936164529361685
ENSE000007343842936687729366947
ENSE000007343852936824129368287
ENSE000008359772934312029343282
ENSE000012733032934544329345540
ENSE000012733262935762329357724
ENSE000013425322937152829371670
ENSE000023771312938111529381172
ENSE000024262652933735229341218
ENSE000036329472934173429341816
ENSE000037853172937011429370222
ENSE000037890042935638229356477

Expression profiles

Bgee: expression breadth ubiquitous, 285 present calls, max score 97.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.9618 / max 842.0722, expressed in 1794 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
13030834.07891794
1303090.8829573

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
buccal mucosa cellCL:000233697.53gold quality
calcaneal tendonUBERON:000370197.12gold quality
colonic epitheliumUBERON:000039796.57gold quality
adrenal tissueUBERON:001830396.54gold quality
islet of LangerhansUBERON:000000696.42gold quality
germinal epithelium of ovaryUBERON:000130496.24gold quality
stromal cell of endometriumCL:000225596.08gold quality
gingival epitheliumUBERON:000194996.08gold quality
superficial temporal arteryUBERON:000161496.07gold quality
oocyteCL:000002395.99gold quality
ventricular zoneUBERON:000305395.71gold quality
tonsilUBERON:000237295.48gold quality
mucosa of paranasal sinusUBERON:000503095.48gold quality
deciduaUBERON:000245095.39gold quality
palpebral conjunctivaUBERON:000181295.18gold quality
tibiaUBERON:000097995.07gold quality
cauda epididymisUBERON:000436094.96gold quality
superior surface of tongueUBERON:000737194.95gold quality
corpus epididymisUBERON:000435994.89gold quality
corpus callosumUBERON:000233694.83gold quality
rectumUBERON:000105294.77gold quality
mammary ductUBERON:000176594.62gold quality
gall bladderUBERON:000211094.56gold quality
ganglionic eminenceUBERON:000402394.49gold quality
endometriumUBERON:000129594.45gold quality
body of pancreasUBERON:000115094.38gold quality
secondary oocyteCL:000065594.29gold quality
seminal vesicleUBERON:000099894.19gold quality
amniotic fluidUBERON:000017394.18gold quality
trigeminal ganglionUBERON:000167594.18gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes21.22
E-GEOD-81383no616.89

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

58 targeting ERGIC2, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4692100.0067.322066
HSA-MIR-451499.9967.101870
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-1213699.9872.815713
HSA-MIR-50799.9770.111915
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-55799.9670.011640
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-4778-3P99.9370.401818
HSA-MIR-205-3P99.9269.923165
HSA-MIR-627-3P99.9071.423316
HSA-MIR-548D-3P99.8770.674362
HSA-MIR-30A-3P99.8769.742928
HSA-MIR-30D-3P99.8769.922917
HSA-MIR-30E-3P99.8769.682942
HSA-MIR-548BB-3P99.8670.584354

Literature-anchored findings (GeneRIF, showing 5)

  • may play an important role in the growth and tumorigenicity of PC-3 prostate tumor cells (PMID:12932305)
  • ERGIC-32 functions as a modulator of the hErv41-hErv46 complex by stabilizing hErv46 (PMID:15308636)
  • Ectopic expression of a partial sequence of PTX1 (Met84 - Leu225) as a VP22-fusion protein in prostate cancer cell line, PC-3, induced cellular senescence. (PMID:16989575)
  • CDA14 participated in the elongation factor 1alpha regulated mechanisms (PMID:17980171)
  • A variant of ERGIC2 with four coding bases deleted has an abrogated function as a transport shuttle, but does continue to upregulate the heme oxygenase 1 gene, suggesting that it may be involved in the oxidative stress pathway. (PMID:24303950)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioERGIC2ENSDARG00000020224
danio_rerioergic2ENSDARG00000051936
mus_musculusErgic2ENSMUSG00000030304
rattus_norvegicusErgic2ENSRNOG00000001852
drosophila_melanogasterCG4293FBGN0024983
caenorhabditis_elegansWBGENE00007668

Paralogs (2): ERGIC1 (ENSG00000113719), ERGIC3 (ENSG00000125991)

Protein

Protein identifiers

Endoplasmic reticulum-Golgi intermediate compartment protein 2Q96RQ1 (reviewed: Q96RQ1)

All UniProt accessions (10): Q96RQ1, F8VPA6, F8VR88, F8VRW9, F8VUZ2, F8W0R1, H0YHJ8, H0YHS0, H0YI50, H0YI58

UniProt curated annotations — full annotation on UniProt →

Function. Possible role in transport between endoplasmic reticulum and Golgi.

Subunit / interactions. May form a heteromeric complex composed of ERGIC1, ERGIC2 and ERGIC3. Interacts with ERGIC3, the interaction is required for the stable expression of both proteins. May interact with EEF1A1.

Subcellular location. Endoplasmic reticulum-Golgi intermediate compartment membrane. Golgi apparatus. cis-Golgi network membrane. Endoplasmic reticulum membrane. Cytoplasm. Nucleus.

Tissue specificity. Ubiquitously expressed.

Similarity. Belongs to the ERGIC family.

RefSeq proteins (1): NP_057654* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR012936Erv_CDomain
IPR039542Erv_NDomain
IPR045888ErvFamily

Pfam: PF07970, PF13850

UniProt features (9 total): topological domain 3, sequence conflict 3, transmembrane region 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96RQ1-F181.210.39

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 163 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, TAATAAT_MIR126, GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP, IVANOVA_HEMATOPOIESIS_MATURE_CELL, GOBP_VESICLE_MEDIATED_TRANSPORT, chr12p11, WEI_MYCN_TARGETS_WITH_E_BOX, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, GOCC_COATED_VESICLE, CUI_TCF21_TARGETS_2_DN, ACEVEDO_LIVER_CANCER_UP, NUYTTEN_EZH2_TARGETS_DN, GOCC_TRANSPORTER_COMPLEX, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum (GO:0006890), vesicle-mediated transport (GO:0016192)

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

GO Cellular Component (12): nucleus (GO:0005634), nucleolus (GO:0005730), cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), COPII-coated ER to Golgi transport vesicle (GO:0030134), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), retrograde cargo receptor complex, Golgi to ER (GO:0061852), transporter complex (GO:1990351), Golgi membrane (GO:0000139)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
intracellular membrane-bounded organelle3
Golgi vesicle transport2
cellular anatomical structure2
endomembrane system2
bounding membrane of organelle2
intercellular transport1
intracellular transport1
transport1
cellular process1
binding1
nuclear lumen1
intracellular membraneless organelle1
intracellular anatomical structure1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
coated vesicle1
endoplasmic reticulum-Golgi intermediate compartment1
cargo receptor complex1
protein-containing complex1
Golgi apparatus1

Protein interactions and networks

STRING

2180 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ERGIC2ERGIC3Q9Y282941
ERGIC2UBN1Q9NPG3846
ERGIC2RNF215Q9Y6U7595
ERGIC2TMPRSS12Q86WS5571
ERGIC2RER1O15258544
ERGIC2CCDC61Q9Y6R9531
ERGIC2BET1O15155527
ERGIC2SURF4O15260506
ERGIC2LMAN1P49257480
ERGIC2ZNF10P21506473
ERGIC2SEC13P55735470
ERGIC2STX5Q13190461
ERGIC2RAB8BQ92930448
ERGIC2ZNF382Q96SR6442
ERGIC2KDELR1P24390420

IntAct

116 interactions, top by confidence:

ABTypeScore
SIL1HSPA5psi-mi:“MI:0914”(association)0.740
COPG1COPB2psi-mi:“MI:0914”(association)0.730
PPP2R5APPP2R1Bpsi-mi:“MI:0914”(association)0.670
COPG1COPEpsi-mi:“MI:0914”(association)0.640
HSD17B2ERGIC2psi-mi:“MI:0915”(physical association)0.640
ZFPL1PPP2R5Epsi-mi:“MI:0914”(association)0.640
ERGIC2ERGIC3psi-mi:“MI:0915”(physical association)0.560
ERGIC3ERGIC2psi-mi:“MI:0915”(physical association)0.560
ERGIC2psi-mi:“MI:0915”(physical association)0.550
LPAR1TMEM223psi-mi:“MI:0914”(association)0.530
SPPL2BUQCRQpsi-mi:“MI:0914”(association)0.530
ENPP7TUBB3psi-mi:“MI:0914”(association)0.530
TM2D2TMEM97psi-mi:“MI:0914”(association)0.530
YIPF3TMEM120Bpsi-mi:“MI:0914”(association)0.530
PPP2R5AAXIN1psi-mi:“MI:0914”(association)0.530
CHRNDTPST2psi-mi:“MI:0914”(association)0.530
SLC22A15ZFPL1psi-mi:“MI:0914”(association)0.530
VAMP5NBASpsi-mi:“MI:0914”(association)0.530
DLK1SCAMP3psi-mi:“MI:0914”(association)0.530
CRHBPTNIP1psi-mi:“MI:0914”(association)0.530
GHITMMFN2psi-mi:“MI:0914”(association)0.530
envPGRMC1psi-mi:“MI:0914”(association)0.460
ERGIC2MAGT1psi-mi:“MI:0915”(physical association)0.400
HSCBRBP5psi-mi:“MI:0914”(association)0.350
YIPF3TMEM223psi-mi:“MI:0914”(association)0.350

BioGRID (289): ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Proximity Label-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS), ERGIC2 (Affinity Capture-MS)

ESM2 similar proteins: A5A6J8, A5D7U4, O18824, O35114, O35409, P05026, P05027, P05028, P06583, P07340, P08251, P13638, P14094, P14231, P14415, P16671, P26201, P27615, P51168, P58421, P70110, P70627, P97943, Q07969, Q08857, Q14108, Q28030, Q2HZ96, Q4R4V5, Q4R5C3, Q5F362, Q5J583, Q5R8S8, Q60417, Q61009, Q6P9A2, Q708S3, Q708S7, Q7T2D4, Q8L8W0

Diamond homologs: P39727, Q09895, Q4R5C3, Q4R8X1, Q54DW2, Q5EAE0, Q5R8G3, Q66KH2, Q6NS19, Q6NVS2, Q7T2D4, Q803I2, Q96RQ1, Q9CQE7, Q9CR89, Q9Y282, O94283

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 161 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Lysosphingolipid and LPA receptors533.7×9e-06
Signaling by GSK3beta mutants533.7×9e-06
CTNNB1 S33 mutants aren’t phosphorylated533.7×9e-06
CTNNB1 S37 mutants aren’t phosphorylated533.7×9e-06
CTNNB1 S45 mutants aren’t phosphorylated533.7×9e-06
CTNNB1 T41 mutants aren’t phosphorylated533.7×9e-06
Beta-catenin phosphorylation cascade529.7×2e-05
Signaling by WNT in cancer526.6×3e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance47
Likely benign2
Benign1

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
4796686NM_016570.3(ERGIC2):c.572+5G>APathogenic

SpliceAI

1886 predictions. Top by Δscore:

VariantEffectΔscore
12:29345441:AC:Adonor_gain1.0000
12:29345442:CC:Cdonor_gain1.0000
12:29349070:AATAC:Adonor_loss1.0000
12:29349071:ATAC:Adonor_loss1.0000
12:29349072:TACTT:Tdonor_loss1.0000
12:29349073:AC:Adonor_loss1.0000
12:29349074:C:Adonor_loss1.0000
12:29349075:T:TGdonor_loss1.0000
12:29349076:TA:Tdonor_loss1.0000
12:29349077:A:ACdonor_gain1.0000
12:29349077:A:AGdonor_loss1.0000
12:29349077:ACGAT:Adonor_gain1.0000
12:29349078:C:CTdonor_gain1.0000
12:29349078:C:Tdonor_loss1.0000
12:29349078:CG:Cdonor_gain1.0000
12:29349078:CGA:Cdonor_gain1.0000
12:29349078:CGAT:Cdonor_gain1.0000
12:29349078:CGATC:Cdonor_gain1.0000
12:29349174:TAAG:Tacceptor_gain1.0000
12:29349178:C:CCacceptor_gain1.0000
12:29350008:CTTA:Cdonor_loss1.0000
12:29350009:TTA:Tdonor_loss1.0000
12:29350010:TA:Tdonor_loss1.0000
12:29350011:A:ACdonor_gain1.0000
12:29350011:ACA:Adonor_loss1.0000
12:29350011:ACATT:Adonor_gain1.0000
12:29350012:C:CTdonor_gain1.0000
12:29350012:CA:Cdonor_gain1.0000
12:29350012:CAT:Cdonor_gain1.0000
12:29350012:CATT:Cdonor_gain1.0000

AlphaMissense

2500 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:29343236:A:TI291K1.000
12:29343239:C:TG290E1.000
12:29343240:C:AG290W1.000
12:29356398:G:CH186D1.000
12:29368258:A:TV82D1.000
12:29343197:A:TV304D0.999
12:29343232:A:CF292L0.999
12:29343232:A:TF292L0.999
12:29343234:A:GF292L0.999
12:29343236:A:CI291R0.999
12:29343240:C:GG290R0.999
12:29343240:C:TG290R0.999
12:29343278:C:GR277P0.999
12:29349145:A:GS221P0.999
12:29349163:G:CH215D0.999
12:29350038:A:CH201Q0.999
12:29350038:A:TH201Q0.999
12:29350040:G:CH201D0.999
12:29356385:C:AG190V0.999
12:29356385:C:TG190D0.999
12:29356386:C:GG190R0.999
12:29356394:A:CI187R0.999
12:29356394:A:TI187K0.999
12:29356396:G:CH186Q0.999
12:29356396:G:TH186Q0.999
12:29356402:A:CN184K0.999
12:29356402:A:TN184K0.999
12:29356406:C:TG183E0.999
12:29356407:C:AG183W0.999
12:29356414:T:AK180N0.999

dbSNP variants (sampled 300 via entrez): RS1000037745 (12:29341653 G>A), RS1000145425 (12:29356730 G>A), RS1000202987 (12:29374121 T>C), RS1000212584 (12:29379649 T>C), RS1000244337 (12:29361304 T>C), RS1000331513 (12:29375708 A>C,G), RS1000429801 (12:29342110 C>G), RS1000507718 (12:29348776 GCA>G), RS1000522114 (12:29347426 T>C), RS1000649452 (12:29341544 C>T), RS1000706250 (12:29355161 A>G), RS1000787998 (12:29380770 G>C), RS1000807551 (12:29362332 T>C), RS1000837848 (12:29368592 C>T), RS1000963276 (12:29355732 T>C)

Disease associations

OMIM: gene MIM:612236 | disease phenotypes: MIM:607812

GenCC curated gene-disease

Mondo (1): craniolenticulosutural dysplasia (MONDO:0011911)

Orphanet (1): Craniolenticulosutural dysplasia (Orphanet:50814)

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST006103_5Interleukin-6 levels3.000000e-06
GCST006661_121Male-pattern baldness5.000000e-16
GCST009391_1784Metabolite levels9.000000e-07
GCST90000025_1032Appendicular lean mass2.000000e-16

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0004810interleukin-6 measurement
EFO:0004468glucose measurement
EFO:0010477fructose measurement
EFO:0010481galactose measurement
EFO:0004980appendicular lean mass

MeSH disease descriptors (1)

DescriptorNameTree numbers
C564332Craniolenticulosutural Dysplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, decreases methylation3
Cyclosporineincreases expression3
sodium arseniteincreases abundance, increases expression2
Acetaminophendecreases expression, increases expression2
aristolochic acid Idecreases expression1
bisphenol Faffects cotreatment, decreases methylation1
dicrotophosdecreases expression1
bisphenol Adecreases expression1
trichostatin Aaffects expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
perfluorooctane sulfonic aciddecreases expression1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression1
jinfukangdecreases expression1
Zoledronic Aciddecreases expression1
Fulvestrantdecreases methylation, affects cotreatment1
Arsenicincreases abundance, increases expression1
Doxorubicindecreases expression1
Formaldehydedecreases expression1
Manganesedecreases expression1
Quercetindecreases expression1
Dihydrotestosteroneincreases expression1
Tetrachlorodibenzodioxindecreases expression1
Thimerosalincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Aflatoxin B1decreases methylation1
Aflatoxin M1decreases expression1
Cadmium Chloridedecreases expression1
Copper Sulfatedecreases expression1
Lactic Aciddecreases expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_B1RGAbcam HeLa ERGIC2 KOCancer cell lineFemale

Clinical trials (associated diseases)

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

  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): craniolenticulosutural dysplasia