EMC3

gene
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Summary

EMC3 (ER membrane protein complex subunit 3, HGNC:23999) is a protein-coding gene on chromosome 3p25.3, encoding ER membrane protein complex subunit 3 (Q9P0I2). Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins. It is a selective cancer dependency (DepMap: 79.4% of cell lines).

Contributes to membrane insertase activity. Involved in protein insertion into ER membrane by stop-transfer membrane-anchor sequence and tail-anchored membrane protein insertion into ER membrane. Located in endoplasmic reticulum membrane. Part of EMC complex.

Source: NCBI Gene 55831 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 36 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 79.4% of screened cell lines
  • MANE Select transcript: NM_001394674

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23999
Approved symbolEMC3
NameER membrane protein complex subunit 3
Location3p25.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000125037
Ensembl biotypeprotein_coding
OMIM620273
Entrez55831

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 6 protein_coding, 2 retained_intron, 1 protein_coding_CDS_not_defined, 1 nonsense_mediated_decay

ENST00000245046, ENST00000429759, ENST00000470827, ENST00000487465, ENST00000497557, ENST00000685575, ENST00000686016, ENST00000693754, ENST00000881006, ENST00000881007

RefSeq mRNA: 2 — MANE Select: NM_001394674 NM_001394674, NM_018447

CCDS: CCDS2594

Canonical transcript exons

ENST00000245046 — 8 exons

ExonStartEnd
ENSE0000085211599697199969801
ENSE0000132459799626829964197
ENSE0000190146399865079986841
ENSE0000347180299773899977446
ENSE0000353538199736289973709
ENSE0000361157499769579977050
ENSE0000362092399705829970661
ENSE0000368829499743849974488

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 98.40.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 58.8229 / max 423.8560, expressed in 1826 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
4101056.74261826
410131.7430909
410110.176062
410140.161353

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
triceps brachiiUBERON:000150998.40gold quality
gluteal muscleUBERON:000200098.34gold quality
monocyteCL:000057698.21gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.21gold quality
gastrocnemiusUBERON:000138898.16gold quality
biceps brachiiUBERON:000150798.15gold quality
mononuclear cellCL:000084298.03gold quality
muscle of legUBERON:000138397.90gold quality
leukocyteCL:000073897.85gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451197.82gold quality
muscle organUBERON:000163097.60gold quality
hindlimb stylopod muscleUBERON:000425297.59gold quality
heart right ventricleUBERON:000208097.21gold quality
islet of LangerhansUBERON:000000697.12gold quality
stromal cell of endometriumCL:000225597.02gold quality
diaphragmUBERON:000110397.00gold quality
vastus lateralisUBERON:000137996.89gold quality
skeletal muscle tissueUBERON:000113496.83gold quality
quadriceps femorisUBERON:000137796.71gold quality
olfactory segment of nasal mucosaUBERON:000538696.68gold quality
bloodUBERON:000017896.50gold quality
rectumUBERON:000105296.50gold quality
deltoidUBERON:000147696.45gold quality
heart left ventricleUBERON:000208496.23gold quality
cardiac ventricleUBERON:000208296.13gold quality
adrenal tissueUBERON:001830396.12gold quality
trabecular bone tissueUBERON:000248396.10gold quality
left testisUBERON:000453396.10gold quality
right atrium auricular regionUBERON:000663195.97gold quality
right testisUBERON:000453495.88gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-13yes11.61
E-MTAB-9221yes10.90
E-HCAD-9yes5.67
E-MTAB-7606no681.97
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

56 targeting EMC3, 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-5011-5P100.0083.465820
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-477599.9875.006394
HSA-MIR-548AN99.9770.912817
HSA-MIR-426799.9666.532368
HSA-MIR-548AT-5P99.9670.832666
HSA-MIR-6778-3P99.9667.292693
HSA-MIR-6809-3P99.9171.453814
HSA-MIR-4753-3P99.9071.033786
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-469899.8471.414303
HSA-MIR-132399.8369.892471
HSA-MIR-3680-3P99.7572.513095
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-4677-5P99.7070.091940
HSA-MIR-378A-5P99.6566.331311
HSA-MIR-450299.6566.991021
HSA-MIR-6848-3P99.6466.49885
HSA-MIR-3679-3P99.6469.881599
HSA-MIR-3942-3P99.5769.032854
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-444199.4966.563216
HSA-MIR-516A-3P99.4667.961378
HSA-MIR-516B-3P99.4667.961378
HSA-MIR-7162-5P99.4668.081368
HSA-MIR-150-3P99.4370.51920
HSA-MIR-431899.3866.941505
HSA-MIR-2116-5P99.3269.341273

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 79.4% of screened cell lines.

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioemc3ENSDARG00000020607
mus_musculusEmc3ENSMUSG00000030286
rattus_norvegicusEmc3ENSRNOG00000009934
drosophila_melanogasterEMC3FBGN0032292
caenorhabditis_elegansWBGENE00013378

Protein

Protein identifiers

ER membrane protein complex subunit 3Q9P0I2 (reviewed: Q9P0I2)

Alternative names: Transmembrane protein 111

All UniProt accessions (5): Q9P0I2, A0A8I5KPL4, A0A8I5KS41, A0A8I5KU67, S4R3U9

UniProt curated annotations — full annotation on UniProt →

Function. Part of the endoplasmic reticulum membrane protein complex (EMC) that enables the energy-independent insertion into endoplasmic reticulum membranes of newly synthesized membrane proteins. Preferentially accommodates proteins with transmembrane domains that are weakly hydrophobic or contain destabilizing features such as charged and aromatic residues. Involved in the cotranslational insertion of multi-pass membrane proteins in which stop-transfer membrane-anchor sequences become ER membrane spanning helices. It is also required for the post-translational insertion of tail-anchored/TA proteins in endoplasmic reticulum membranes. By mediating the proper cotranslational insertion of N-terminal transmembrane domains in an N-exo topology, with translocated N-terminus in the lumen of the ER, controls the topology of multi-pass membrane proteins like the G protein-coupled receptors. By regulating the insertion of various proteins in membranes, it is indirectly involved in many cellular processes.

Subunit / interactions. Component of the ER membrane protein complex (EMC).

Subcellular location. Endoplasmic reticulum membrane.

Similarity. Belongs to the EMC3 family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9P0I2-11yes
Q9P0I2-22

RefSeq proteins (2): NP_001381603, NP_060917 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002809EMC3/TMCO1Family
IPR008568EMC3Family

Pfam: PF01956

UniProt features (43 total): helix 14, mutagenesis site 9, strand 6, sequence conflict 4, topological domain 4, transmembrane region 3, initiator methionine 1, chain 1, splice variant 1

Structure

Experimental structures (PDB)

10 structures.

PDBMethodResolution (Å)
8J0OELECTRON MICROSCOPY3.32
7ADOELECTRON MICROSCOPY3.39
6WW7ELECTRON MICROSCOPY3.4
8EOIELECTRON MICROSCOPY3.4
8J0NELECTRON MICROSCOPY3.47
7ADPELECTRON MICROSCOPY3.6
8S9SELECTRON MICROSCOPY3.6
9ZZ6ELECTRON MICROSCOPY4.16
6Z3WELECTRON MICROSCOPY6.4
9C7VELECTRON MICROSCOPY6.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P0I2-F178.380.22

Functional residue map

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

Mutagenesis-validated functional residues (9):

PositionPhenotype
31no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
31no effect on emc assembly and no effect on membrane insertion of hydrophobic transmembrane helices-containing proteins b
101no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
106no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
110no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
111no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
173no effect on emc assembly and no effect on membrane insertion of hydrophobic transmembrane helices-containing proteins b
180no effect on emc assembly but decreased membrane insertion of hydrophobic transmembrane helices-containing proteins by t
180no effect on emc assembly and no effect on membrane insertion of hydrophobic transmembrane helices-containing proteins b

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-8980692RHOA GTPase cycle

MSigDB gene sets: 174 (showing top): E2F_Q4, E2F4DP1_01, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, TGACCTY_ERR1_Q2, E2F1DP1_01, E2F1DP2_01, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, PETRETTO_BLOOD_PRESSURE_UP, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, RYTTCCTG_ETS2_B, GOBP_MEMBRANE_ORGANIZATION, GOBP_ENDOPLASMIC_RETICULUM_ORGANIZATION, GOBP_LOCALIZATION_WITHIN_MEMBRANE, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN

GO Biological Process (2): protein insertion into ER membrane by stop-transfer membrane-anchor sequence (GO:0045050), tail-anchored membrane protein insertion into ER membrane (GO:0071816)

GO Molecular Function (2): protein binding (GO:0005515), membrane insertase activity (GO:0032977)

GO Cellular Component (4): endoplasmic reticulum membrane (GO:0005789), membrane (GO:0016020), EMC complex (GO:0072546), endoplasmic reticulum (GO:0005783)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
RHO GTPase cycle1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein insertion into ER membrane2
binding1
establishment of protein localization to membrane1
protein carrier activity1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
cellular anatomical structure1
endoplasmic reticulum membrane1
membrane protein complex1
endoplasmic reticulum protein-containing complex1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1

Protein interactions and networks

STRING

918 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EMC3EMC6Q9BV81904
EMC3EMC2Q15006895
EMC3EMC1Q8N766892
EMC3EMC4Q5J8M3891
EMC3MMGT1Q8N4V1885
EMC3EMC7Q9NPA0827
EMC3GET1O00258795
EMC3EMC8O43402794
EMC3EMC9Q9Y3B6774
EMC3DERL2Q9GZP9758
EMC3OXA1LQ15070733
EMC3EMC10Q5UCC4710
EMC3TMCO1Q9UM00690
EMC3UBAC2Q8NBM4685
EMC3GET3O43681606

IntAct

109 interactions, top by confidence:

ABTypeScore
EMC2EMC8psi-mi:“MI:0914”(association)0.940
EMC8EMC2psi-mi:“MI:0914”(association)0.940
EMC3EMC2psi-mi:“MI:0915”(physical association)0.860
EMC2EMC10psi-mi:“MI:0914”(association)0.800
EMC7EMC8psi-mi:“MI:0914”(association)0.790
EMC3EMC8psi-mi:“MI:0914”(association)0.730
MMGT1EMC8psi-mi:“MI:0914”(association)0.730
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
EMC1EMC8psi-mi:“MI:0914”(association)0.640
TRDNTMEM223psi-mi:“MI:0914”(association)0.640
EMC4EMC8psi-mi:“MI:0914”(association)0.640
SLC12A2CLGNpsi-mi:“MI:0914”(association)0.640
EMC10EMC8psi-mi:“MI:0915”(physical association)0.620
MTAPEMC3psi-mi:“MI:0915”(physical association)0.560

BioGRID (211): EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC9 (Affinity Capture-MS), UBQLN2 (Affinity Capture-MS), EMC8 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC1 (Affinity Capture-MS), EMC7 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC3 (Affinity Capture-MS)

ESM2 similar proteins: A8N0V8, B2RZ37, C0HLM6, D3Z7Q2, F1MDB2, O35092, O49636, O60830, O80840, O95563, P00130, P08200, P0CM24, P0CM25, P11024, P38718, P39515, P59670, Q00765, Q13423, Q29RM3, Q2HJE9, Q3ZCB8, Q5BIN4, Q5M7K0, Q5R4Z3, Q5R7C1, Q5RE33, Q5U2V8, Q5U4U5, Q60870, Q61941, Q68EQ9, Q6INE8, Q6PBX9, Q6ZL94, Q7SXW4, Q8L7H8, Q8LD38, Q8N5G0

Diamond homologs: A7A082, B3LQQ2, B5VLV9, P36039, Q3ZCB8, Q54YN3, Q5R7C1, Q5U2V8, Q7SXW4, Q99KI3, Q9P0I2, Q9P787

SIGNOR signaling

2 interactions.

AEffectBMechanism
EMC3“form complex”“Endoplasmic reticulum membrane complex- EMC9 variant”binding
EMC3“form complex”“Endoplasmic reticulum membrane complex, EMC8 variant”binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 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
Defective CFTR causes cystic fibrosis515.5×4e-03
Anchoring of the basal body to the plasma membrane914.3×5e-06

GO biological processes:

GO termPartnersFoldFDR
tail-anchored membrane protein insertion into ER membrane986.9×7e-14
ERAD pathway916.8×6e-07
cilium assembly86.1×6e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance21
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1242 predictions. Top by Δscore:

VariantEffectΔscore
3:9964194:CTGT:Cacceptor_gain1.0000
3:9964218:C:Tacceptor_gain1.0000
3:9970576:TCTTA:Tdonor_loss1.0000
3:9970577:CTTAC:Cdonor_loss1.0000
3:9970578:TTACC:Tdonor_loss1.0000
3:9970579:TACCA:Tdonor_loss1.0000
3:9970580:A:Tdonor_loss1.0000
3:9970581:C:CAdonor_loss1.0000
3:9970657:TCACC:Tacceptor_gain1.0000
3:9970658:CACC:Cacceptor_gain1.0000
3:9970658:CACCC:Cacceptor_gain1.0000
3:9970659:ACC:Aacceptor_gain1.0000
3:9970660:CC:Cacceptor_gain1.0000
3:9970660:CCC:Cacceptor_gain1.0000
3:9970661:CC:Cacceptor_gain1.0000
3:9970662:C:CCacceptor_gain1.0000
3:9970671:C:CTacceptor_gain1.0000
3:9973705:CTTGG:Cacceptor_gain1.0000
3:9974382:A:ACdonor_gain1.0000
3:9974383:C:CCdonor_gain1.0000
3:9977051:C:CCacceptor_gain1.0000
3:9977442:CTTGA:Cacceptor_gain1.0000
3:9986503:TGA:Tdonor_loss1.0000
3:9986504:GACCT:Gdonor_loss1.0000
3:9986505:ACCTG:Adonor_loss1.0000
3:9986506:C:CGdonor_loss1.0000
3:9964195:TGT:Tacceptor_gain0.9900
3:9964197:TCT:Tacceptor_loss0.9900
3:9964198:C:CAacceptor_loss0.9900
3:9964198:C:CCacceptor_gain0.9900

AlphaMissense

1736 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:9964185:C:GA224P1.000
3:9970620:A:GL179P1.000
3:9970623:C:TG178E1.000
3:9970635:A:GL174P1.000
3:9970635:A:TL174H1.000
3:9970645:A:GW171R1.000
3:9970645:A:TW171R1.000
3:9973675:C:AK149N1.000
3:9973675:C:GK149N1.000
3:9973678:A:CF148L1.000
3:9973678:A:TF148L1.000
3:9973679:A:GF148S1.000
3:9973680:A:GF148L1.000
3:9973696:A:CF142L1.000
3:9973696:A:TF142L1.000
3:9973698:A:GF142L1.000
3:9974389:A:TV136D1.000
3:9974391:A:CF135L1.000
3:9974391:A:TF135L1.000
3:9974393:A:GF135L1.000
3:9974417:A:GW127R1.000
3:9974417:A:TW127R1.000
3:9974422:C:TG125D1.000
3:9977428:G:CS58R1.000
3:9977428:G:TS58R1.000
3:9977430:T:GS58R1.000
3:9970620:A:TL179H0.999
3:9970624:C:GG178R0.999
3:9970624:C:TG178R0.999
3:9970625:A:CF177L0.999

dbSNP variants (sampled 300 via entrez): RS1000041788 (3:9963006 C>A), RS1000078926 (3:9980878 G>C), RS1000202791 (3:9975504 G>C), RS1000235520 (3:9980449 T>C), RS1000289192 (3:10007052 T>C), RS1000305352 (3:9982364 C>T), RS1000374148 (3:9986414 C>A,T), RS1000466282 (3:9974321 T>C,G), RS1000573300 (3:9979101 C>T), RS1000626481 (3:9982185 C>A,G,T), RS1000678041 (3:10004105 G>T), RS1000765082 (3:9990789 A>G), RS1000783703 (3:10004676 T>A), RS1000970499 (3:9976511 C>T), RS1000971877 (3:9962624 G>A)

Disease associations

OMIM: gene MIM:620273 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067207 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.00Kd10.02nMCHEMBL5653589
8.00ED5010.02nMCHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide2148318: Binding affinity to human EMC3 incubated for 45 mins by Kinobead based pull down assaykd0.0100uM

CTD chemical–gene interactions

27 total (human), top 27 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, increases abundance, increases expression2
Benzo(a)pyreneaffects methylation, increases expression2
Nickeldecreases expression2
Valproic Acidincreases expression2
Cadmium Chlorideincreases expression2
dicrotophosdecreases expression1
cobaltous chlorideincreases expression1
zinc chromateincreases expression, increases abundance1
manganese chlorideincreases expression, affects cotreatment, increases abundance1
chromium hexavalent ionincreases abundance, increases expression1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)increases expression1
Vorinostatdecreases expression1
Acetaminophenincreases expression1
Arsenicaffects cotreatment, increases abundance, increases expression1
Drugs, Chinese Herbalincreases expression1
Hydrogen Peroxideincreases expression, affects cotreatment1
Ivermectindecreases expression1
Manganeseaffects cotreatment, increases abundance, increases expression1
Smokedecreases expression1
Theophyllineaffects cotreatment, increases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
Cyclosporineincreases expression1
Sodium Selenitedecreases expression1
Copper Sulfateincreases expression1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651360BindingBinding affinity to human EMC3 incubated for 45 mins by Kinobead based pull down assayNVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

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.