ITM2C

gene
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Also known as BRI3E25hRPC.1050_D_4ITM3BRICD2C

Summary

ITM2C (integral membrane protein 2C, HGNC:6175) is a protein-coding gene on chromosome 2q37.1, encoding Integral membrane protein 2C (Q9NQX7). Negative regulator of amyloid-beta peptide production.

Enables amyloid-beta binding activity. Involved in negative regulation of neuron projection development and neuron differentiation. Located in several cellular components, including Golgi apparatus; lysosome; and perinuclear region of cytoplasm.

Source: NCBI Gene 81618 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 62 total
  • MANE Select transcript: NM_030926

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:6175
Approved symbolITM2C
Nameintegral membrane protein 2C
Location2q37.1
Locus typegene with protein product
StatusApproved
AliasesBRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C
Ensembl geneENSG00000135916
Ensembl biotypeprotein_coding
OMIM609554
Entrez81618

Gene structure

Transcript identifiers

Ensembl transcripts: 10 — 9 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000326407, ENST00000326427, ENST00000335005, ENST00000409704, ENST00000418408, ENST00000457215, ENST00000492029, ENST00000541852, ENST00000543957, ENST00000620962

RefSeq mRNA: 5 — MANE Select: NM_030926 NM_001012514, NM_001012516, NM_001287240, NM_001287241, NM_030926

CCDS: CCDS2479, CCDS33395, CCDS33396, CCDS74665

Canonical transcript exons

ENST00000326427 — 6 exons

ExonStartEnd
ENSE00000922497230877400230877550
ENSE00001868342230878008230879248
ENSE00001899015230864942230865145
ENSE00003548237230873417230873557
ENSE00003611891230875620230875808
ENSE00003784419230876857230876967

Expression profiles

Bgee: expression breadth ubiquitous, 275 present calls, max score 99.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 164.2906 / max 1966.1830, expressed in 1811 samples.

FANTOM5 promoters (13 alternative TSS)

Promoter IDTPM avgSamples expressed
25828151.39671793
258275.29331563
258292.4477817
258311.3348580
258300.7148338
258320.5243288
258340.4790277
258380.4667232
258370.4142208
258330.4096223

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
nucleus accumbensUBERON:000188299.66gold quality
mucosa of transverse colonUBERON:000499199.66gold quality
anterior cingulate cortexUBERON:000983599.60gold quality
cingulate cortexUBERON:000302799.59gold quality
caudate nucleusUBERON:000187399.56gold quality
amygdalaUBERON:000187699.53gold quality
lateral globus pallidusUBERON:000247699.53gold quality
prefrontal cortexUBERON:000045199.47gold quality
rectumUBERON:000105299.47gold quality
hypothalamusUBERON:000189899.46gold quality
putamenUBERON:000187499.42gold quality
right frontal lobeUBERON:000281099.38gold quality
Brodmann (1909) area 9UBERON:001354099.34gold quality
transverse colonUBERON:000115799.28gold quality
dorsolateral prefrontal cortexUBERON:000983499.17gold quality
colonic mucosaUBERON:000031799.12gold quality
pituitary glandUBERON:000000799.11gold quality
frontal cortexUBERON:000187099.09gold quality
adenohypophysisUBERON:000219699.09gold quality
mucosa of sigmoid colonUBERON:000499399.09gold quality
neocortexUBERON:000195099.01gold quality
forebrainUBERON:000189098.97gold quality
Ammon’s hornUBERON:000195498.97gold quality
telencephalonUBERON:000189398.96gold quality
substantia nigraUBERON:000203898.93gold quality
spinal cordUBERON:000224098.90gold quality
C1 segment of cervical spinal cordUBERON:000646998.88gold quality
midbrainUBERON:000189198.85gold quality
temporal lobeUBERON:000187198.83gold quality
substantia nigra pars reticulataUBERON:000196698.83gold quality

Single-cell (SCXA)

Detected in 46 experiment(s), a significant marker in 38.

ExperimentMarker?Max mean expression
E-GEOD-125970yes2451.42
E-CURD-120yes1734.99
E-MTAB-9467yes1551.01
E-HCAD-10yes1520.22
E-GEOD-150728yes1467.01
E-GEOD-149689yes1438.55
E-MTAB-8410yes1325.94
E-MTAB-9154yes1319.79
E-HCAD-32yes1300.46
E-CURD-77yes1223.15
E-MTAB-7407yes1138.29
E-HCAD-4yes1017.62
E-MTAB-10553yes899.47
E-CURD-55yes852.80
E-MTAB-9221yes826.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting ITM2C, 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-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-9-5P100.0072.282361
HSA-MIR-6798-5P100.0065.77699
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-1252-5P100.0069.802774
HSA-MIR-453199.9969.703181
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-4666A-3P99.9671.713434
HSA-MIR-6721-5P99.9368.922981
HSA-MIR-218-5P99.9372.222103
HSA-MIR-381-3P99.9371.872854
HSA-MIR-30099.9271.762856
HSA-MIR-205-3P99.9269.923165
HSA-MIR-464899.9167.00710
HSA-MIR-627-3P99.9071.423316
HSA-MIR-605-3P99.8869.221833
HSA-MIR-449299.8768.253611
HSA-MIR-1211999.8768.351653
HSA-MIR-659-3P99.8570.691620
HSA-MIR-63699.8069.581500
HSA-MIR-548AJ-5P99.7871.123085
HSA-MIR-548F-5P99.7871.023093
HSA-MIR-548G-5P99.7871.123085
HSA-MIR-548X-5P99.7871.123085
HSA-MIR-197699.7465.481127
HSA-MIR-430699.7270.503630

Literature-anchored findings (GeneRIF, showing 1)

  • Unlocking the Potential of the CA2, CA7, and ITM2C Gene Signatures for the Early Detection of Colorectal Cancer: A Comprehensive Analysis of RNA-Seq Data by Utilizing Machine Learning Algorithms. (PMID:37895185)

Cross-species orthologs

6 orthologs

OrganismSymbolGene ID
danio_rerioitm2cbENSDARG00000039650
danio_rerioitm2caENSDARG00000043448
mus_musculusItm2cENSMUSG00000026223
rattus_norvegicusItm2cENSRNOG00000017359
drosophila_melanogasterCG3662FBGN0031285
caenorhabditis_elegansWBGENE00016106

Paralogs (2): ITM2A (ENSG00000078596), ITM2B (ENSG00000136156)

Protein

Protein identifiers

Integral membrane protein 2CQ9NQX7 (reviewed: Q9NQX7)

Alternative names: Cerebral protein 14, Transmembrane protein BRI3

All UniProt accessions (6): B8ZZM6, C9JG41, E7EUS6, F5H4I5, Q96JS4, Q9NQX7

UniProt curated annotations — full annotation on UniProt →

Function. Negative regulator of amyloid-beta peptide production. May inhibit the processing of APP by blocking its access to alpha- and beta-secretase. Binding to the beta-secretase-cleaved APP C-terminal fragment is negligible, suggesting that ITM2C is a poor gamma-secretase cleavage inhibitor. May play a role in TNF-induced cell death and neuronal differentiation.

Subunit / interactions. Interacts with BACE1. Interacts with APP. Interacts with STMN2.

Subcellular location. Lysosome membrane. Cell membrane.

Tissue specificity. High levels in the brain, specifically in the cerebral cortex, medulla, amygdala, hippocampus, thalamus, caudate nucleus, cerebellum, olfactory lobe and spinal cord. Very low levels in other organs.

Post-translational modifications. Type I membrane-bound, as well as soluble, furin has a pre-eminent role in ITM2C proteolytic processing. PCSK7 and PCSK5 may also be involved although to a lesser extent. The soluble form of PCSK7 is incapable of processing ITM2C. Fails to undergo shedding by ADAM10 and intramembrane cleavage by SPPL2B.

Similarity. Belongs to the ITM2 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9NQX7-11yes
Q9NQX7-22
Q9NQX7-33

RefSeq proteins (5): NP_001012532, NP_001012534, NP_001274169, NP_001274170, NP_112188* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR007084BRICHOS_domDomain
IPR040145ITM2Family

Pfam: PF04089

UniProt features (15 total): sequence conflict 3, splice variant 2, chain 1, peptide 1, sequence variant 1, mutagenesis site 1, transmembrane region 1, domain 1, site 1, modified residue 1, glycosylation site 1, disulfide bond 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9NQX7-F177.120.42

Functional residue map

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

Catalytic / active sites (1): 242–243 (cleavage; by furin)

Post-translational modifications (1): 37

Disulfide bonds (1): 163–222

Glycosylation sites (1): 169

Mutagenesis-validated functional residues (1):

PositionPhenotype
241–242completely abrogates proteolytic processing.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 488 (showing top): GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, VERHAAK_AML_WITH_NPM1_MUTATED_DN, REACTOME_INNATE_IMMUNE_SYSTEM, MODULE_255, GOCC_VACUOLAR_MEMBRANE, GOCC_SECRETORY_GRANULE, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, MODULE_317, LINDGREN_BLADDER_CANCER_CLUSTER_3_DN, GOBP_EXTRINSIC_APOPTOTIC_SIGNALING_PATHWAY, GOBP_NEUROGENESIS, HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION

GO Biological Process (4): negative regulation of neuron projection development (GO:0010977), neuron differentiation (GO:0030182), negative regulation of amyloid precursor protein biosynthetic process (GO:0042985), positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)

GO Molecular Function (3): amyloid-beta binding (GO:0001540), ATP binding (GO:0005524), protein binding (GO:0005515)

GO Cellular Component (7): lysosome (GO:0005764), lysosomal membrane (GO:0005765), Golgi apparatus (GO:0005794), plasma membrane (GO:0005886), perinuclear region of cytoplasm (GO:0048471), extracellular exosome (GO:0070062), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm2
cellular anatomical structure2
regulation of neuron projection development1
neuron projection development1
negative regulation of cell projection organization1
cell differentiation1
generation of neurons1
negative regulation of glycoprotein biosynthetic process1
amyloid precursor protein biosynthetic process1
regulation of amyloid precursor protein biosynthetic process1
extrinsic apoptotic signaling pathway1
positive regulation of apoptotic signaling pathway1
regulation of extrinsic apoptotic signaling pathway1
peptide binding1
adenyl ribonucleotide binding1
purine ribonucleoside triphosphate binding1
binding1
lytic vacuole1
lysosome1
lytic vacuole membrane1
endomembrane system1
intracellular membrane-bounded organelle1
membrane1
cell periphery1
extracellular vesicle1

Protein interactions and networks

STRING

1026 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ITM2CBACE1P56817752
ITM2CPCSK7Q16549748
ITM2CCLPTM1O96005611
ITM2CFURINP09958589
ITM2CSLC35A5Q9BS91525
ITM2CKNDC1Q76NI1513
ITM2CKIAA1755Q5JYT7454
ITM2CPDZD11Q5EBL8431
ITM2CINSYN1Q2T9L4410
ITM2CERBB2P04626399
ITM2CSYT11Q9BT88391
ITM2CEPB41L4AQ9HCS5388
ITM2CMED31Q9Y3C7371
ITM2CEML6Q6ZMW3363
ITM2CGAS2L3Q86XJ1359

IntAct

75 interactions, top by confidence:

ABTypeScore
TSPAN15ADAM10psi-mi:“MI:0914”(association)0.840
TSPAN5ADAM10psi-mi:“MI:0914”(association)0.800
APPAPBB1psi-mi:“MI:0914”(association)0.740
CFTRESYT2psi-mi:“MI:2364”(proximity)0.710
SLC39A5FAM171A2psi-mi:“MI:0914”(association)0.640
MTNR1BIRS4psi-mi:“MI:0914”(association)0.530
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
TIMP3ZZEF1psi-mi:“MI:0914”(association)0.530
ANKHFAM234Bpsi-mi:“MI:0914”(association)0.530
CFTRITM2Cpsi-mi:“MI:0915”(physical association)0.520
NRASESYT2psi-mi:“MI:2364”(proximity)0.480
ITM2CDlg4psi-mi:“MI:0407”(direct interaction)0.440
RNF7ITM2Cpsi-mi:“MI:0915”(physical association)0.370
psi-mi:“MI:0914”(association)0.350
ESYT2psi-mi:“MI:0914”(association)0.350
PGRMC1psi-mi:“MI:0914”(association)0.350
SNAP23psi-mi:“MI:0914”(association)0.350
HAX1psi-mi:“MI:0914”(association)0.350
APPRTL1psi-mi:“MI:0914”(association)0.350
Mpsi-mi:“MI:0914”(association)0.350
NS3C15orf61psi-mi:“MI:0914”(association)0.350
SHTN1psi-mi:“MI:0914”(association)0.350
TMEM223psi-mi:“MI:0914”(association)0.350
TNFRSF10Apsi-mi:“MI:0914”(association)0.350
POMKESYT2psi-mi:“MI:0914”(association)0.350
SCN2AIGLL5psi-mi:“MI:0914”(association)0.350

BioGRID (134): ITM2C (Affinity Capture-MS), MVB12B (Affinity Capture-MS), ITM2C (Two-hybrid), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), MVB12B (Affinity Capture-MS), ITM2C (Reconstituted Complex), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), ITM2C (Proximity Label-MS), ITM2C (Affinity Capture-MS), ITM2C (Two-hybrid), ITM2C (Two-hybrid), CXCL9 (Two-hybrid), FNDC9 (Two-hybrid)

ESM2 similar proteins: A2VDN0, A5A6H8, B5DFM7, E9Q9F6, O18638, O42204, O43736, O88393, O89051, P0DP43, P21841, P26342, P58239, Q03167, Q06890, Q06AV4, Q14CH0, Q29TV8, Q3T0P7, Q4R540, Q52N47, Q5NVC3, Q5PQL7, Q5R876, Q5SC59, Q5SC60, Q5SY80, Q5XIE8, Q60HC1, Q61500, Q6AYE5, Q6GPK2, Q6P7C7, Q6P995, Q6W3E5, Q71SY6, Q802A9, Q86XM0, Q86XP6, Q8BGN6

Diamond homologs: A2VDN0, A5A6H8, O42204, O43736, O89051, Q06AV4, Q3T0P7, Q4R540, Q52N47, Q5NVC3, Q5PQL7, Q5R876, Q5XIE8, Q60HC1, Q61500, Q91VK4, Q9NQX7, Q9Y287

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance39
Likely benign2
Benign2

Top pathogenic / likely-pathogenic (0)

SpliceAI

885 predictions. Top by Δscore:

VariantEffectΔscore
2:230865144:GG:Gdonor_gain1.0000
2:230865145:GG:Gdonor_gain1.0000
2:230865146:G:GGdonor_gain1.0000
2:230875608:C:CAacceptor_gain1.0000
2:230875613:T:TAacceptor_gain1.0000
2:230875617:CAG:Cacceptor_loss1.0000
2:230875618:A:AGacceptor_gain1.0000
2:230875618:AGC:Aacceptor_loss1.0000
2:230875618:AGCT:Aacceptor_gain1.0000
2:230875618:AGCTG:Aacceptor_gain1.0000
2:230875619:G:GAacceptor_gain1.0000
2:230875619:GC:Gacceptor_gain1.0000
2:230875619:GCT:Gacceptor_gain1.0000
2:230875619:GCTG:Gacceptor_gain1.0000
2:230875619:GCTGG:Gacceptor_gain1.0000
2:230875805:GCGG:Gdonor_gain1.0000
2:230875807:GG:Gdonor_gain1.0000
2:230875808:GG:Gdonor_gain1.0000
2:230875809:G:GGdonor_gain1.0000
2:230875809:GTG:Gdonor_loss1.0000
2:230875810:T:Adonor_loss1.0000
2:230876852:GCCA:Gacceptor_loss1.0000
2:230876853:CCAG:Cacceptor_loss1.0000
2:230876854:CA:Cacceptor_loss1.0000
2:230876855:A:ACacceptor_loss1.0000
2:230876855:A:AGacceptor_gain1.0000
2:230876855:AG:Aacceptor_gain1.0000
2:230876855:AGG:Aacceptor_gain1.0000
2:230876856:G:GTacceptor_gain1.0000
2:230876856:GG:Gacceptor_gain1.0000

AlphaMissense

1738 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:230875800:T:CF148L1.000
2:230875801:T:GF148C1.000
2:230875802:C:AF148L1.000
2:230875802:C:GF148L1.000
2:230875794:C:GH146D0.999
2:230875801:T:CF148S0.999
2:230876861:T:CL152P0.999
2:230876866:G:CA154P0.999
2:230876869:T:GY155D0.999
2:230876893:T:AC163S0.999
2:230876893:T:CC163R0.999
2:230876894:G:AC163Y0.999
2:230876894:G:CC163S0.999
2:230876894:G:TC163F0.999
2:230876895:C:GC163W0.999
2:230876900:T:AV165D0.999
2:230876909:T:AL168H0.999
2:230877502:T:AC222S0.999
2:230877502:T:CC222R0.999
2:230877503:G:AC222Y0.999
2:230877503:G:CC222S0.999
2:230877503:G:TC222F0.999
2:230877504:C:GC222W0.999
2:230875789:T:AI144N0.998
2:230875789:T:CI144T0.998
2:230875789:T:GI144S0.998
2:230875795:A:CH146P0.998
2:230875796:T:AH146Q0.998
2:230875796:T:GH146Q0.998
2:230875798:A:CD147A0.998

dbSNP variants (sampled 300 via entrez): RS1000416614 (2:230868292 G>A), RS1000548826 (2:230864035 G>A,T), RS1000571796 (2:230870165 G>A), RS1000972729 (2:230875151 C>A), RS1000996914 (2:230864399 G>A,T), RS1001151902 (2:230869399 C>T), RS1001178782 (2:230871137 G>T), RS1001228166 (2:230865844 C>T), RS1001229758 (2:230873684 C>T), RS1001233646 (2:230865482 TGGGG>T,TGGG,TGGGGG), RS1001279224 (2:230866017 G>A,C,T), RS1001297753 (2:230877750 T>C), RS1001682952 (2:230868961 C>A), RS1001702041 (2:230873863 G>A), RS1001736680 (2:230868745 C>T)

Disease associations

OMIM: gene MIM:609554 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

StudyTraitp-value
GCST90002390_468Mean corpuscular hemoglobin2.000000e-12
GCST90002392_176Mean corpuscular volume7.000000e-13
GCST90002396_183Mean reticulocyte volume1.000000e-09
GCST90002397_464Mean spheric corpuscular volume7.000000e-11

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004527mean corpuscular hemoglobin
EFO:0010701mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Aincreases methylation, decreases expression, affects expression, affects cotreatment4
Arsenicaffects methylation, decreases ubiquitination, increases methylation, decreases expression, increases abundance4
Valproic Acidaffects expression, increases expression, increases methylation4
sodium arsenitedecreases expression, increases abundance, increases expression2
Benzo(a)pyreneaffects methylation, increases expression2
Phenylmercuric Acetateaffects cotreatment, increases expression2
Cyclosporinedecreases expression2
TAK-243increases sumoylation1
lead acetateincreases expression1
beta-lapachonedecreases expression1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
2-bromopalmitatedecreases reaction, increases abundance, increases palmitoylation1
beta-methylcholineaffects expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
ICG 001increases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
(+)-JQ1 compounddecreases expression1
MT19c compounddecreases expression1
Fulvestrantincreases methylation, affects cotreatment1
Acetaminophenincreases expression1
Atrazineincreases expression1
Cadmiumdecreases reaction, increases abundance, increases palmitoylation1
Cytarabinedecreases expression1
Dichlorodiphenyl Dichloroethylenedecreases expression1
Doxorubicinincreases expression1
Estradiolaffects cotreatment, decreases expression1
Gallic Aciddecreases expression1
Ivermectindecreases expression1
Leadaffects expression1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

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

CellosaurusNameCategorySex
CVCL_E0FMUbigene HeLa ITM2C KOCancer cell lineFemale

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.