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ITM2C integral membrane protein 2C [ Homo sapiens (human) ]

Gene ID: 81618, updated on 27-Nov-2024

Summary

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Official Symbol
ITM2Cprovided by HGNC
Official Full Name
integral membrane protein 2Cprovided by HGNC
Primary source
HGNC:HGNC:6175
See related
Ensembl:ENSG00000135916 MIM:609554; AllianceGenome:HGNC:6175
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
E25; BRI3; E25C; ITM3; BRICD2C
Summary
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. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in colon (RPKM 478.6), brain (RPKM 266.8) and 17 other tissues See more
Orthologs
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Genomic context

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See ITM2C in Genome Data Viewer
Location:
2q37.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (230864185..230879254)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (231347355..231362416)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (231728900..231743969)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene calcium binding protein 39 Neighboring gene BANF1 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17248 Neighboring gene RNA, U6 small nuclear 268, pseudogene Neighboring gene Sharpr-MPRA regulatory region 14077 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231654665-231655164 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:231657991-231659190 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17249 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12413 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr2:231708391-231709016 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231726605-231727215 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231728341-231728999 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:231729658-231730316 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231730317-231730973 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734265-231734922 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231734923-231735580 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17250 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17251 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12417 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231742513-231743287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17253 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231757691-231758270 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231758271-231758850 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12418 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12419 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr2:231773167-231774366 Neighboring gene GPR55 cis regulatory suppressor of immune response RNA Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:231789302-231790090 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17259 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12421 Neighboring gene G protein-coupled receptor 55 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804174-231804714 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:231804715-231805254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17260 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17261 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17262 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17263 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17264 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17265 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12422 Neighboring gene COX20 pseudogene 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A catalogue of genes in the cardiovascular system as identified by expressed sequence tags. Liew CC, et al. Proc Natl Acad Sci U S A, 1994 Oct 25. PMID 7938007, Free PMC Article
  2. Sequence, genomic structure and tissue expression of Human BRI3, a member of the BRI gene family. Vidal R, et al. Gene, 2001 Mar 21. PMID 11290423
  3. 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. Maurya NS, et al. Genes (Basel), 2023 Sep 22. PMID 37895185, Free PMC Article
  4. Isolation of markers for chondro-osteogenic differentiation using cDNA library subtraction. Molecular cloning and characterization of a gene belonging to a novel multigene family of integral membrane proteins. Deleersnijder W, et al. J Biol Chem, 1996 Aug 9. PMID 8702637
  5. BRI3 inhibits amyloid precursor protein processing in a mechanistically distinct manner from its homologue dementia gene BRI2. Matsuda S, et al. J Biol Chem, 2009 Jun 5. PMID 19366692, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  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.
    Title: 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.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of genetic variants with hemorrhagic stroke in Japanese individuals.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables amyloid-beta binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables amyloid-beta binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of amyloid precursor protein biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of neuron projection development IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neuron differentiation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of extrinsic apoptotic signaling pathway IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in Golgi apparatus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
  
located_in extracellular exosome HDA PubMed 
located_in lysosomal membrane IEA
Inferred from Electronic Annotation
more info
  
located_in lysosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in perinuclear region of cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
integral membrane protein 2C
Names
BRICHOS domain containing 2C
cerebral protein 14
integral membrane protein 3
transmembrane protein BRI3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001012514.3 → NP_001012532.1  integral membrane protein 2C isoform 3

    See identical proteins and their annotated locations for NP_001012532.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
    Source sequence(s)
    AK056321, BC098563, DA182471
    Consensus CDS
    CCDS33396.1
    UniProtKB/Swiss-Prot
    Q9NQX7
    Related
    ENSP00000335121.6, ENST00000335005.10
    Conserved Domains (1) summary
    smart01039
    Location:89 → 181
    BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

  2. NM_001012516.2 → NP_001012534.1  integral membrane protein 2C isoform 2

    See identical proteins and their annotated locations for NP_001012534.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the central coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
    Source sequence(s)
    AK056321, BC098563, DA138409
    Consensus CDS
    CCDS33395.1
    UniProtKB/TrEMBL
    B4DIB1
    Related
    ENSP00000322100.6, ENST00000326407.10
    Conserved Domains (1) summary
    cl04394
    Location:136 → 191
    BRICHOS; BRICHOS domain

  3. NM_001287240.2 → NP_001274169.1  integral membrane protein 2C isoform 4

    See identical proteins and their annotated locations for NP_001274169.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in its 5' UTR and initiates translation from a downstream start codon, compared to variant 1. The encoded isoform (4) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AC012507, AF272043, BC098563, BX444331
    Consensus CDS
    CCDS74665.1
    UniProtKB/TrEMBL
    B8ZZM6
    Related
    ENSP00000387242.2, ENST00000409704.6
    Conserved Domains (1) summary
    smart01039
    Location:74 → 166
    BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

  4. NM_001287241.2 → NP_001274170.1  integral membrane protein 2C isoform 1

    See identical proteins and their annotated locations for NP_001274170.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Both variants 1 and 5 encode the same isoform (1).
    Source sequence(s)
    AC012507, AF272043, BC098563, BX444331
    Consensus CDS
    CCDS2479.1
    UniProtKB/Swiss-Prot
    B3KPG4, Q4G0A8, Q53H84, Q6IAE7, Q86VK5, Q8N288, Q8TAW0, Q9BUP8, Q9NQX7
    UniProtKB/TrEMBL
    B4DIB1
    Conserved Domains (1) summary
    smart01039
    Location:136 → 228
    BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

  5. NM_030926.6 → NP_112188.1  integral membrane protein 2C isoform 1

    See identical proteins and their annotated locations for NP_112188.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 5 encode the same isoform.
    Source sequence(s)
    AF272043, BC098563
    Consensus CDS
    CCDS2479.1
    UniProtKB/Swiss-Prot
    B3KPG4, Q4G0A8, Q53H84, Q6IAE7, Q86VK5, Q8N288, Q8TAW0, Q9BUP8, Q9NQX7
    UniProtKB/TrEMBL
    B4DIB1
    Related
    ENSP00000322730.6, ENST00000326427.11
    Conserved Domains (1) summary
    smart01039
    Location:136 → 228
    BRICHOS; The BRICHOS domain is found in a variety of proteins implicated in dementia, respiratory distress and cancer

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    230864185..230879254
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    231347355..231362416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NQX7.1 GenPept UniProtKB/Swiss-Prot:Q9NQX7

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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