EMC2

gene
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Summary

EMC2 (ER membrane protein complex subunit 2, HGNC:28963) is a protein-coding gene on chromosome 8q23.1, encoding ER membrane protein complex subunit 2 (Q15006). 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: 20.0% 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. Is extrinsic component of endoplasmic reticulum membrane. Part of EMC complex.

Source: NCBI Gene 9694 — RefSeq curated summary.

At a glance

  • GWAS associations: 5
  • Clinical variants (ClinVar): 47 total
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 20.0% of screened cell lines
  • MANE Select transcript: NM_014673

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:28963
Approved symbolEMC2
NameER membrane protein complex subunit 2
Location8q23.1
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000104412
Ensembl biotypeprotein_coding
OMIM607722
Entrez9694

Gene structure

Transcript identifiers

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

ENST00000220853, ENST00000517593, ENST00000517784, ENST00000519450, ENST00000519642, ENST00000520294, ENST00000524143, ENST00000890427, ENST00000890428, ENST00000890429

RefSeq mRNA: 4 — MANE Select: NM_014673 NM_001329493, NM_001329494, NM_001329495, NM_014673

CCDS: CCDS6309

Canonical transcript exons

ENST00000220853 — 11 exons

ExonStartEnd
ENSE00001130722108443624108443698
ENSE00002097848108486512108489196
ENSE00003489653108450428108450492
ENSE00003509694108470062108470121
ENSE00003523467108455873108455930
ENSE00003535617108469826108469911
ENSE00003574064108449823108449936
ENSE00003576346108479006108479110
ENSE00003579331108475882108475963
ENSE00003652475108453062108453147
ENSE00003664948108476782108476892

Expression profiles

Bgee: expression breadth ubiquitous, 299 present calls, max score 98.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 47.9333 / max 2279.5144, expressed in 1799 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
9025147.00401797
902500.9293520

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370198.41gold quality
C1 segment of cervical spinal cordUBERON:000646997.97gold quality
corpus callosumUBERON:000233697.73gold quality
spinal cordUBERON:000224097.45gold quality
spermCL:000001997.18gold quality
descending thoracic aortaUBERON:000234596.64gold quality
hindlimb stylopod muscleUBERON:000425296.41gold quality
right coronary arteryUBERON:000162596.32gold quality
body of pancreasUBERON:000115096.30gold quality
right atrium auricular regionUBERON:000663196.30gold quality
popliteal arteryUBERON:000225096.26gold quality
tibial arteryUBERON:000761096.26gold quality
islet of LangerhansUBERON:000000696.15gold quality
aortaUBERON:000094796.10gold quality
arteryUBERON:000163796.07gold quality
rectumUBERON:000105296.01gold quality
cranial nerve IIUBERON:000094195.97gold quality
mucosa of stomachUBERON:000119995.97gold quality
thoracic aortaUBERON:000151595.97gold quality
ascending aortaUBERON:000149695.96gold quality
lateral globus pallidusUBERON:000247695.96gold quality
left coronary arteryUBERON:000162695.95gold quality
subthalamic nucleusUBERON:000190695.93gold quality
gall bladderUBERON:000211095.82gold quality
lower esophagus muscularis layerUBERON:003583395.82gold quality
lower esophagusUBERON:001347395.79gold quality
colonic epitheliumUBERON:000039795.70gold quality
right lungUBERON:000216795.63gold quality
putamenUBERON:000187495.60gold quality
esophagogastric junction muscularis propriaUBERON:003584195.58gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting EMC2, 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-190A-3P100.0080.355520
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-391099.9571.132227
HSA-MIR-1236-3P99.9468.041695
HSA-MIR-1213299.4768.901341
HSA-MIR-4666A-5P99.4169.721887
HSA-MIR-20B-3P99.2967.05784
HSA-MIR-126499.2566.811317
HSA-MIR-7151-3P99.0469.722370
HSA-MIR-143-5P98.9868.87946
HSA-MIR-4709-3P98.8868.041594
HSA-MIR-513B-3P98.7668.121577
HSA-MIR-118398.7567.101116
HSA-MIR-3689A-5P98.3570.121049
HSA-MIR-3689B-5P98.3570.121049
HSA-MIR-3689E98.3570.121049
HSA-MIR-3689F98.3570.081052
HSA-MIR-197297.6767.381172
HSA-MIR-428697.2064.371587
HSA-MIR-873-3P96.8466.09786

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 20.0% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • We then examined the oncogenic effects of the RSPO2-EMC2 fusion gene and confirmed that it can drive oncogenesis, sustain tumor growth and promote metastasis. (PMID:30250044)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioemc2ENSDARG00000003308
mus_musculusEmc2ENSMUSG00000022337
rattus_norvegicusEmc2ENSRNOG00000005123
drosophila_melanogasterEMC2BFBGN0038461
drosophila_melanogasterEMC2AFBGN0038462
caenorhabditis_elegansWBGENE00021973

Protein

Protein identifiers

ER membrane protein complex subunit 2Q15006 (reviewed: Q15006)

Alternative names: Tetratricopeptide repeat protein 35

All UniProt accessions (3): Q15006, E5RGJ2, H0YAS9

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). Interacts with WNK1 (via amphipathic alpha-helix region); promoting the ER membrane protein complex assembly by preventing EMC2 ubiquitination.

Subcellular location. Endoplasmic reticulum membrane.

Post-translational modifications. Ubiquitinated when soluble in the cytoplasm, leading to its degradation by the proteasome. Interaction with EMC2 prevents its ubiquitination and degradation.

Similarity. Belongs to the EMC2 family.

RefSeq proteins (4): NP_001316422, NP_001316423, NP_001316424, NP_055488* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR011990TPR-like_helical_dom_sfHomologous_superfamily
IPR019734TPR_rptRepeat
IPR039856EMC2-likeFamily
IPR055217TPR_EMC2Domain

Pfam: PF22890

UniProt features (41 total): helix 18, mutagenesis site 13, repeat 3, strand 2, modified residue 2, initiator methionine 1, chain 1, sequence conflict 1

Structure

Experimental structures (PDB)

11 structures.

PDBMethodResolution (Å)
6Y4LX-RAY DIFFRACTION2.2
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-Q15006-F194.400.85

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): 2, 255

Mutagenesis-validated functional residues (13):

PositionPhenotype
122no effect on transmembrane domain binding of tail-anchored proteins; when associated with k-61 and k-95.
156loss of interaction with emc5.
160loss of interaction with emc5.
171decreased interaction with emc5 and emc8.
180decreased interaction with emc3.
189–191decreased transmembrane domain binding of tail-anchored proteins.
193–194no effect on transmembrane domain binding of tail-anchored proteins.
200decreased interaction with emc5 and emc8.
227loss of interaction with emc5 and emc8.
259decreased interaction with emc3.
28loss of interaction with emc5.
61no effect on transmembrane domain binding of tail-anchored proteins; when associated with k-95 and e-122.
95no effect on transmembrane domain binding of tail-anchored proteins; when associated with k-61 and e-122.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 157 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, ONKEN_UVEAL_MELANOMA_UP, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, INGRAM_SHH_TARGETS_DN, GOBP_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE, GOBP_ENDOMEMBRANE_SYSTEM_ORGANIZATION, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOBP_MEMBRANE_ORGANIZATION, GOBP_ENDOPLASMIC_RETICULUM_ORGANIZATION, BURTON_ADIPOGENESIS_12, GOBP_LOCALIZATION_WITHIN_MEMBRANE, GOBP_PROTEIN_INSERTION_INTO_MEMBRANE, BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN, GOCC_EXTRINSIC_COMPONENT_OF_ORGANELLE_MEMBRANE

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 (6): cytoplasm (GO:0005737), endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), extrinsic component of endoplasmic reticulum membrane (GO:0042406), EMC complex (GO:0072546), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein insertion into ER membrane2
cellular anatomical structure2
endoplasmic reticulum membrane2
binding1
establishment of protein localization to membrane1
protein carrier activity1
intracellular anatomical structure1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
extrinsic component of organelle membrane1
membrane protein complex1
endoplasmic reticulum protein-containing complex1

Protein interactions and networks

STRING

1430 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
EMC2EMC6Q9BV81932
EMC2EMC1Q8N766926
EMC2EMC4Q5J8M3920
EMC2EMC3Q9P0I2895
EMC2MMGT1Q8N4V1873
EMC2EMC8O43402771
EMC2DERL2Q9GZP9760
EMC2EMC9Q9Y3B6742
EMC2EMC10Q5UCC4710
EMC2EMC7Q9NPA0710
EMC2ATP5MC3P48201622
EMC2RPL8P25120621
EMC2ACSF2Q96CM8621
EMC2UBAC2Q8NBM4618
EMC2CISD1Q9NZ45546

IntAct

187 interactions, top by confidence:

ABTypeScore
EMC9EMC2psi-mi:“MI:0915”(physical association)0.940
EMC2EMC9psi-mi:“MI:0915”(physical association)0.940
EMC2EMC8psi-mi:“MI:0915”(physical association)0.940
EMC2EMC8psi-mi:“MI:0914”(association)0.940
EMC8EMC2psi-mi:“MI:0915”(physical association)0.940
EMC8EMC2psi-mi:“MI:0914”(association)0.940
EMC3EMC2psi-mi:“MI:0915”(physical association)0.860
MMGT1EMC2psi-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

BioGRID (596): EMC8 (Two-hybrid), IKZF3 (Two-hybrid), EMC9 (Two-hybrid), CCDC33 (Two-hybrid), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC2 (Affinity Capture-MS), EMC3 (Affinity Capture-MS), EMC10 (Affinity Capture-MS), EMC6 (Affinity Capture-MS), MMGT1 (Affinity Capture-MS)

ESM2 similar proteins: A0MT11, A1Z3X3, A2VD00, A4GWN3, A4II09, A4QNE0, A4VCH4, B5KFI0, O35841, P23116, P49754, Q09161, Q0P5I8, Q14152, Q15006, Q15386, Q1JU68, Q3B8M3, Q5E993, Q5E9L7, Q5KU39, Q5R4J9, Q5R644, Q5R882, Q5RE70, Q5XI83, Q5ZJZ6, Q5ZKG8, Q5ZMW3, Q68E01, Q6GLK9, Q6N069, Q6NRL4, Q6PCR7, Q6TGY8, Q6WKZ8, Q7L5D6, Q7TPD0, Q80UM3, Q8BHL5

Diamond homologs: B0BNG0, O60110, Q15006, Q5E993, Q5M7J9, Q5R882, Q6INS3, Q6TGY8, Q8AVU9, Q9CRD2, Q86K48

SIGNOR signaling

2 interactions.

AEffectBMechanism
EMC2“form complex”“Endoplasmic reticulum membrane complex- EMC9 variant”binding
EMC2“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 157 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
PD-L1(CD274) glycosylation and translocation to plasma membrane526.8×2e-04
Regulation of CDH1 posttranslational processing and trafficking to plasma membrane517.3×1e-03
Maturation of spike protein616.4×2e-04
Maturation of DENV proteins715.3×1e-04
Defective CFTR causes cystic fibrosis511.3×7e-03

GO biological processes:

GO termPartnersFoldFDR
tail-anchored membrane protein insertion into ER membrane964.3×2e-12
ERAD pathway1115.2×5e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2113 predictions. Top by Δscore:

VariantEffectΔscore
8:108449817:TTTCA:Tacceptor_loss1.0000
8:108449818:TTCAG:Tacceptor_loss1.0000
8:108449819:TCAGA:Tacceptor_loss1.0000
8:108449820:CAG:Cacceptor_loss1.0000
8:108449821:A:AGacceptor_gain1.0000
8:108449821:AG:Aacceptor_loss1.0000
8:108449822:G:GTacceptor_gain1.0000
8:108449822:GA:Gacceptor_gain1.0000
8:108449822:GAA:Gacceptor_gain1.0000
8:108449822:GAAA:Gacceptor_gain1.0000
8:108449822:GAAAT:Gacceptor_gain1.0000
8:108449885:G:GTdonor_gain1.0000
8:108449932:TGATA:Tdonor_gain1.0000
8:108449933:GATA:Gdonor_gain1.0000
8:108449933:GATAG:Gdonor_gain1.0000
8:108449934:ATA:Adonor_gain1.0000
8:108449935:TA:Tdonor_gain1.0000
8:108449936:AGTAA:Adonor_loss1.0000
8:108449937:G:GGdonor_gain1.0000
8:108449937:G:Tdonor_loss1.0000
8:108450416:A:AGacceptor_gain1.0000
8:108450416:AT:Aacceptor_gain1.0000
8:108450416:ATGT:Aacceptor_gain1.0000
8:108450417:T:Gacceptor_gain1.0000
8:108450426:A:AGacceptor_gain1.0000
8:108450426:AGTTT:Aacceptor_gain1.0000
8:108450427:G:GAacceptor_gain1.0000
8:108450427:GT:Gacceptor_gain1.0000
8:108450427:GTT:Gacceptor_gain1.0000
8:108450427:GTTT:Gacceptor_gain1.0000

AlphaMissense

1974 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
8:108449892:G:AG37E1.000
8:108450430:T:AW53R1.000
8:108450430:T:CW53R1.000
8:108450460:G:CA63P1.000
8:108453078:T:CL79P1.000
8:108453089:T:CF83L1.000
8:108453091:C:AF83L1.000
8:108453091:C:GF83L1.000
8:108453106:A:CR88S1.000
8:108453106:A:TR88S1.000
8:108453122:G:CG94R1.000
8:108453123:G:AG94D1.000
8:108453137:G:CA99P1.000
8:108469838:C:AR126S1.000
8:108469839:G:CR126P1.000
8:108469893:T:CL144P1.000
8:108469905:T:CL148P1.000
8:108470084:T:AW158R1.000
8:108470084:T:CW158R1.000
8:108470094:T:CL161P1.000
8:108475892:G:CA174P1.000
8:108475903:T:GC177W1.000
8:108475914:T:CL181P1.000
8:108475959:C:AA196D1.000
8:108476882:G:AG231E1.000
8:108449850:G:CR23T0.999
8:108449850:G:TR23I0.999
8:108449851:A:CR23S0.999
8:108449851:A:TR23S0.999
8:108449891:G:AG37R0.999

dbSNP variants (sampled 300 via entrez): RS1000123960 (8:108456043 TAAA>T,TAA,TAAAA), RS1000141446 (8:108477612 A>C,G), RS1000271665 (8:108472114 T>C), RS1000274174 (8:108471341 T>G), RS1000289146 (8:108449438 A>G), RS1000302681 (8:108472454 A>T), RS1000412524 (8:108464905 A>G,T), RS1000469442 (8:108460066 C>G), RS1000544160 (8:108460385 CT>C), RS1000583644 (8:108478805 C>G), RS1000684376 (8:108454182 T>G), RS1000709279 (8:108470976 T>C), RS1000805680 (8:108489334 C>T), RS1000836762 (8:108489035 A>G), RS1000873510 (8:108447929 T>A)

Disease associations

OMIM: gene MIM:607722 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

5 associations (top):

StudyTraitp-value
GCST002545_2Ossification of the posterior longitudinal ligament of the spine2.000000e-13
GCST003983_17Male-pattern baldness4.000000e-13
GCST006661_172Male-pattern baldness2.000000e-11
GCST006661_282Male-pattern baldness5.000000e-27
GCST010703_334Brain morphology (MOSTest)2.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6066426 (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
6.48Kd331.1nMCHEMBL5653589
6.48ED50331.1nMCHEMBL5653589

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]benzamide2148317: Binding affinity to human EMC2 incubated for 45 mins by Kinobead based pull down assaykd0.3311uM

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases expression, affects expression2
aristolochic acid Idecreases expression1
dicrotophosdecreases expression1
arseniteaffects binding, increases reaction1
sodium arsenitedecreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
epigallocatechin gallateaffects cotreatment, decreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic aciddecreases expression1
bisphenol Sdecreases methylation1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Dichlorodiphenyl Dichloroethyleneincreases expression1
Ivermectindecreases expression1
Tamoxifenaffects expression1
Valproic Aciddecreases methylation1
Cyclosporineincreases expression1
Aflatoxin B1decreases methylation1
Okadaic Aciddecreases expression1
Particulate Matterdecreases expression, increases abundance1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL5651359BindingBinding affinity to human EMC2 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_B1R3Abcam HeLa EMC2 KOCancer cell lineFemale
CVCL_E1W0HAP1 EMC2 (-)Cancer cell lineMale

Clinical trials (associated diseases)

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