Aliases for ITM2C Gene

Aliases for ITM2C Gene

  • Integral Membrane Protein 2C 2 3 4 5
  • BRI3 2 3 4
  • BRICHOS Domain Containing 2C 2 3
  • Transmembrane Protein BRI3 3 4
  • Cerebral Protein 14 3 4
  • BRICD2C 2 3
  • ITM3 2 3
  • E25 2 3
  • Integral Membrane Protein 3 3
  • HRPC.1050_D_4 2
  • ITM2C 5
  • E25C 3

External Ids for ITM2C Gene

Previous GeneCards Identifiers for ITM2C Gene

  • GC02U990099
  • GC02P230461
  • GC02P231693
  • GC02P231932
  • GC02P231555
  • GC02P231437
  • GC02P223571
  • GC02P231729

Summaries for ITM2C Gene

GeneCards Summary for ITM2C Gene

ITM2C (Integral Membrane Protein 2C) is a Protein Coding gene. Diseases associated with ITM2C include Cerebral Amyloid Angiopathy, Itm2b-Related, 1 and Cerebral Amyloid Angiopathy, Itm2b-Related, 2. Gene Ontology (GO) annotations related to this gene include amyloid-beta binding. An important paralog of this gene is ITM2B.

UniProtKB/Swiss-Prot Summary for ITM2C Gene

  • 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 (By similarity).

Gene Wiki entry for ITM2C Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ITM2C Gene

Genomics for ITM2C Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ITM2C Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J230863 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 259 +5.3 5289 11.6 SP1 IKZF1 ZNF600 JUND POLR2A ZNF223 ZNF10 ZIC2 NFIC MXD4 ITM2C ENSG00000261096 COPS7B LINC00471 ENSG00000230385 SPATA3-AS1 SPATA3 PSMD1 HSALNG0022901 GCSIR
GH02J230885 Enhancer 1.1 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.1 +22.3 22316 2.2 MYNN BMI1 RFX1 ATF2 ZNF26 CREB1 ZNF507 EGR2 RAD21 POLR2A GCSIR RPL28P2 COPS7B NCL ITM2C GPR55 ENSG00000230385
GH02J230913 Enhancer 0.8 Ensembl ENCODE 11.7 +50.0 50016 2.8 REST TRIM22 CTCF SMC3 SMARCA5 RAD21 SPI1 RFX5 ELF1 STAT5A GCSIR ITM2C SPATA3 SPATA3-AS1 PSMD1 GPR55 ENSG00000283164 lnc-SPATA3-1
GH02J230893 Enhancer 1 Ensembl ENCODE dbSUPER 6.5 +30.7 30716 3.8 GABPA TAL1 EBF1 BHLHE40 SPI1 MYC MAX ZEB2 IKZF1 TCF12 ITM2C GCSIR ENSG00000230385 GPR55
GH02J230861 Enhancer 0.8 Ensembl ENCODE dbSUPER 7.3 -2.3 -2285 1.4 EBF1 PKNOX1 ARNT TAF1 REST EGR2 ZFHX2 ITM2C HSALNG0022901 HSALNG0022902 CAB39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ITM2C on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ITM2C

Top Transcription factor binding sites by QIAGEN in the ITM2C gene promoter:
  • AP-1
  • Arnt
  • ITF-2
  • MyoD
  • Sp1
  • Spz1
  • SREBP-1a
  • SREBP-1b
  • SREBP-1c
  • Tal-1beta

Genomic Locations for ITM2C Gene

Latest Assembly
chr2:230,864,185-230,879,254
(GRCh38/hg38)
Size:
15,070 bases
Orientation:
Plus strand

Previous Assembly
chr2:231,728,900-231,743,969
(GRCh37/hg19 by Entrez Gene)
Size:
15,070 bases
Orientation:
Plus strand

chr2:231,729,354-231,743,963
(GRCh37/hg19 by Ensembl)
Size:
14,610 bases
Orientation:
Plus strand

Genomic View for ITM2C Gene

Genes around ITM2C on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ITM2C Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ITM2C Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ITM2C Gene

Proteins for ITM2C Gene

  • Protein details for ITM2C Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQX7-ITM2C_HUMAN
    Recommended name:
    Integral membrane protein 2C
    Protein Accession:
    Q9NQX7
    Secondary Accessions:
    • B3KPG4
    • Q4G0A8
    • Q53H84
    • Q6IAE7
    • Q86VK5
    • Q8N288
    • Q8TAW0
    • Q9BUP8

    Protein attributes for ITM2C Gene

    Size:
    267 amino acids
    Molecular mass:
    30224 Da
    Quaternary structure:
    • Interacts with BACE1. Interacts with APP. Interacts with STMN2.

    Alternative splice isoforms for ITM2C Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ITM2C Gene

Post-translational modifications for ITM2C Gene

  • 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.
  • Glycosylation at Asn169
  • Ubiquitination at Lys3, Lys14, Lys20, and Lys187
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ITM2C Gene

Domains & Families for ITM2C Gene

Gene Families for ITM2C Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for ITM2C Gene

InterPro:
Blocks:
  • BRICHOS domain

Suggested Antigen Peptide Sequences for ITM2C Gene

GenScript: Design optimal peptide antigens:
  • Transmembrane protein BRI3 (ITM2C_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9NQX7

UniProtKB/Swiss-Prot:

ITM2C_HUMAN :
  • Belongs to the ITM2 family.
Family:
  • Belongs to the ITM2 family.
genes like me logo Genes that share domains with ITM2C: view

Function for ITM2C Gene

Molecular function for ITM2C Gene

UniProtKB/Swiss-Prot 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 (By similarity).

Phenotypes From GWAS Catalog for ITM2C Gene

Gene Ontology (GO) - Molecular Function for ITM2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001540 amyloid-beta binding IPI 19849849
GO:0005515 protein binding IPI 18452648
GO:0005524 ATP binding IEA --
genes like me logo Genes that share ontologies with ITM2C: view
genes like me logo Genes that share phenotypes with ITM2C: view

Animal Models for ITM2C Gene

MGI Knock Outs for ITM2C:
  • Itm2c Itm2c<tm1b(EUCOMM)Wtsi>

miRNA for ITM2C Gene

miRTarBase miRNAs that target ITM2C

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ITM2C

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for ITM2C Gene

Localization for ITM2C Gene

Subcellular locations from UniProtKB/Swiss-Prot for ITM2C Gene

Lysosome membrane. Single-pass type II membrane protein. Cell membrane. Single-pass type II membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ITM2C gene
Compartment Confidence
plasma membrane 5
lysosome 5
extracellular 4
golgi apparatus 4
cytosol 2
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1
peroxisome 0
nucleus 0

Gene Ontology (GO) - Cellular Components for ITM2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005764 lysosome IEA,IDA 14592447
GO:0005765 lysosomal membrane IEA --
GO:0005794 Golgi apparatus IDA --
GO:0005886 plasma membrane IEA,IDA 19114711
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with ITM2C: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ITM2C Gene

Pathways & Interactions for ITM2C Gene

PathCards logo

SuperPathways for ITM2C Gene

No Data Available

Gene Ontology (GO) - Biological Process for ITM2C Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010977 negative regulation of neuron projection development IDA 18452648
GO:0030182 neuron differentiation IDA 18452648
GO:0042985 negative regulation of amyloid precursor protein biosynthetic process IBA 21873635
GO:2001238 positive regulation of extrinsic apoptotic signaling pathway IEA --
genes like me logo Genes that share ontologies with ITM2C: view

No data available for Pathways by source and SIGNOR curated interactions for ITM2C Gene

Drugs & Compounds for ITM2C Gene

No Compound Related Data Available

Transcripts for ITM2C Gene

mRNA/cDNA for ITM2C Gene

5 REFSEQ mRNAs :
25 NCBI additional mRNA sequence :
10 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ITM2C

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for ITM2C Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8
SP1: -
SP2: - -
SP3: - -
SP4: -
SP5:

Relevant External Links for ITM2C Gene

GeneLoc Exon Structure for
ITM2C

Expression for ITM2C Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ITM2C Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for ITM2C Gene

This gene is overexpressed in Colon - Transverse (x4.6) and Brain - Nucleus accumbens (basal ganglia) (x4.0).

Protein differential expression in normal tissues from HIPED for ITM2C Gene

This gene is overexpressed in Bone (39.7) and Amniocyte (10.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for ITM2C Gene



Protein tissue co-expression partners for ITM2C Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ITM2C

SOURCE GeneReport for Unigene cluster for ITM2C Gene:

Hs.111577

mRNA Expression by UniProt/SwissProt for ITM2C Gene:

Q9NQX7-ITM2C_HUMAN
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.

Evidence on tissue expression from TISSUES for ITM2C Gene

  • Nervous system(5)
  • Intestine(4.9)
  • Kidney(3.8)
  • Stomach(2.8)
  • Lung(2.7)
  • Eye(2.6)
  • Skin(2.5)
  • Spleen(2.3)
genes like me logo Genes that share expression patterns with ITM2C: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for ITM2C Gene

Orthologs for ITM2C Gene

This gene was present in the common ancestor of animals.

Orthologs for ITM2C Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ITM2C 29 30
  • 98.63 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ITM2C 29 30
  • 91.14 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ITM2C 29 30
  • 90.39 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Itm2c 29 16 30
  • 87.64 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Itm2c 29
  • 87.64 (n)
Oppossum
(Monodelphis domestica)
Mammalia ITM2C 30
  • 39 (a)
OneToOne
Chicken
(Gallus gallus)
Aves ITM2C 29 30
  • 70.88 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia ITM2C 30
  • 41 (a)
OneToOne
Zebrafish
(Danio rerio)
Actinopterygii itm2ca 29 30
  • 65.35 (n)
OneToMany
itm2cb 30
  • 42 (a)
OneToMany
wufj35c02 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.2395 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG3662 30
  • 15 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea C25F6.7 30
  • 17 (a)
OneToMany
Species where no ortholog for ITM2C was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for ITM2C Gene

ENSEMBL:
Gene Tree for ITM2C (if available)
TreeFam:
Gene Tree for ITM2C (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ITM2C: view image
Alliance of Genome Resources:
Additional Orthologs for ITM2C

Paralogs for ITM2C Gene

Paralogs for ITM2C Gene

(2) SIMAP similar genes for ITM2C Gene using alignment to 5 proteins:

  • ITM2C_HUMAN
  • B8ZZM6_HUMAN
  • C9JG41_HUMAN
  • E7EUS6_HUMAN
  • F5H4I5_HUMAN
genes like me logo Genes that share paralogs with ITM2C: view

Variants for ITM2C Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ITM2C Gene

SNP ID Clinical significance and condition Chr 02 pos Variation AA Info Type
rs35084476 Benign: not provided 230,877,499(+) C/T
NM_030926.6(ITM2C):c.661C>T (p.Leu221=)
SYNONYMOUS
rs35154063 Benign: not provided 230,877,483(+) G/T
NM_030926.6(ITM2C):c.645G>T (p.Gly215=)
SYNONYMOUS
rs2289235 -- p.Gly53Ser

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ITM2C Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ITM2C Gene

Variant ID Type Subtype PubMed ID
dgv7335n54 CNV loss 21841781
nsv470522 CNV loss 18288195
nsv834565 CNV gain 17160897

Variation tolerance for ITM2C Gene

Residual Variation Intolerance Score: 60.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.89; 35.33% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ITM2C Gene

Human Gene Mutation Database (HGMD)
ITM2C
SNPedia medical, phenotypic, and genealogical associations of SNPs for
ITM2C
Leiden Open Variation Database (LOVD)
ITM2C

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ITM2C Gene

Disorders for ITM2C Gene

MalaCards: The human disease database

(2) MalaCards diseases for ITM2C Gene - From: COP

Disorder Aliases PubMed IDs
cerebral amyloid angiopathy, itm2b-related, 1
  • dementia, familial british; fbd
cerebral amyloid angiopathy, itm2b-related, 2
  • dementia, familial danish; fdd
- elite association - COSMIC cancer census association via MalaCards
Search ITM2C in MalaCards View complete list of genes associated with diseases

Additional Disease Information for ITM2C

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with ITM2C: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ITM2C Gene

Publications for ITM2C Gene

  1. Association of genetic variants with hemorrhagic stroke in Japanese individuals. (PMID: 20198315) Yoshida T … Yamada Y (International journal of molecular medicine 2010) 3 40
  2. Assessment of a polymorphism of SDK1 with hypertension in Japanese Individuals. (PMID: 19851296) Oguri M … Yamada Y (American journal of hypertension 2010) 3 40
  3. Substrate requirements for SPPL2b-dependent regulated intramembrane proteolysis. (PMID: 19114711) Martin L … Haass C (The Journal of biological chemistry 2009) 3 4
  4. BRI3 inhibits amyloid precursor protein processing in a mechanistically distinct manner from its homologue dementia gene BRI2. (PMID: 19366692) Matsuda S … D'Adamio L (The Journal of biological chemistry 2009) 3 4
  5. BRI3 associates with SCG10 and attenuates NGF-induced neurite outgrowth in PC12 cells. (PMID: 18452648) Gong Y … Yuan J (BMB reports 2008) 3 4

Products for ITM2C Gene

Sources for ITM2C Gene