Seroatlas · Human Serome Atlas

EDEM3

ER degradation-enhancing alpha-mannosidase-like protein 3

Also known as: C1orf22, EDEM3_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9BZQ6
Gene: EDEM3
Ensembl: ENSG00000116406
Chromosome: 1
Canonical length: 932 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Endoplasmic reticulum
Secretome location: Intracellular and membrane

OverviewNCBI Gene

Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]

Canonical amino-acid sequenceUniProt

932 residues, UniProt reviewed canonical sequence.

>Q9BZQ6|EDEM3
     1  MSEAGGRGCG SPVPQRARWR LVAATAAFCL VSATSVWTAG AEPMSREEKQ KLGNQVLEMF
    61  DHAYGNYMEH AYPADELMPL TCRGRVRGQE PSRGDVDDAL GKFSLTLIDS LDTLVVLNKT
   121  KEFEDAVRKV LRDVNLDNDV VVSVFETNIR VLGGLLGGHS LAIMLKEKGE YMQWYNDELL
   181  QMAKQLGYKL LPAFNTTSGL PYPRINLKFG IRKPEARTGT ETDTCTACAG TLILEFAALS
   241  RFTGATIFEE YARKALDFLW EKRQRSSNLV GVTINIHTGD WVRKDSGVGA GIDSYYEYLL
   301  KAYVLLGDDS FLERFNTHYD AIMRYISQPP LLLDVHIHKP MLNARTWMDA LLAFFPGLQV
   361  LKGDIRPAIE THEMLYQVIK KHNFLPEAFT TDFRVHWAQH PLRPEFAEST YFLYKATGDP
   421  YYLEVGKTLI ENLNKYARVP CGFAAMKDVR TGSHEDRMDS FFLAEMFKYL YLLFADKEDI
   481  IFDIEDYIFT TEAHLLPLWL STTNQSISKK NTTSEYTELD DSNFDWTCPN TQILFPNDPL
   541  YAQSIREPLK NVVDKSCPRG IIRVEESFRS GAKPPLRARD FMATNPEHLE ILKKMGVSLI
   601  HLKDGRVQLV QHAIQAASSI DAEDGLRFMQ EMIELSSQQQ KEQQLPPRAV QIVSHPFFGR
   661  VVLTAGPAQF GLDLSKHKET RGFVASSKPS NGCSELTNPE AVMGKIALIQ RGQCMFAEKA
   721  RNIQNAGAIG GIVIDDNEGS SSDTAPLFQM AGDGKDTDDI KIPMLFLFSK EGSIILDAIR
   781  EYEEVEVLLS DKAKDRDPEM ENEEQPSSEN DSQNQSGEQI SSSSQEVDLV DQESSEENSL
   841  NSHPESLSLA DMDNAASISP SEQTSNPTEN HETTNLNGEC TDLDNQLQEQ SETEEDSNPN
   901  VSWGKKVQPI DSILADWNED IEAFEMMEKD EL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against EDEM3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.33
Highest tissue expression: 35 nTPM

Expression across tissuesHPA

Tissue

stomach: 35 nTPM
rectum: 23 nTPM
colon: 20 nTPM
placenta: 20 nTPM
liver: 19 nTPM
duodenum: 18 nTPM

Single-cell type

neutrophil progenitors: 506 nCPM
thyrotrophs: 261 nCPM
lactotrophs: 246 nCPM
somatotrophs: 229 nCPM
neutrophils: 207 nCPM
prostatic glandular cells: 170 nCPM

Immune cell

basophil: 4.2 nTPM
non-classical monocyte: 3.5 nTPM
intermediate monocyte: 3.2 nTPM
myeloid DC: 3.1 nTPM
classical monocyte: 3 nTPM
neutrophil: 2.8 nTPM

Brain region

hypothalamus: 17 nTPM
cerebellum: 17 nTPM
midbrain: 16 nTPM
white matter: 15 nTPM
thalamus: 14 nTPM
spinal cord: 14 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about EDEM3.

Disease | AllUniProt

Conditions EDEM3 is implicated in, by any mechanism.

Congenital disorder of glycosylation 2V (CDG2V) MIM:619493

Disease | GeneticClinVar

16 pathogenic / likely-pathogenic of 155 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Congenital disorder of glycosylation, type 2v
Short stature

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.46
gnomAD pLI: 0
gnomAD missense Z: 1.22
DepMap mean gene effect: -0.09
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 9% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads EDEM3 as an antibody target. Whether an autoantibody or antibody against EDEM3 could matter depends on whether native EDEM3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

EDEM3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label EDEM3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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