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    TM2D3 TM2 domain containing 3 [ Homo sapiens (human) ]

    Gene ID: 80213, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TM2D3provided by HGNC
    Official Full Name
    TM2 domain containing 3provided by HGNC
    Primary source
    HGNC:HGNC:24128
    See related
    Ensembl:ENSG00000184277 MIM:610014; AllianceGenome:HGNC:24128
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BLP2
    Summary
    The protein encoded by this gene contains a structural module related to that of the seven transmembrane domain G protein-coupled receptor superfamily. This protein has sequence and structural similarities to the beta-amyloid binding protein (BBP), but, unlike BBP, it does not regulate a response to beta-amyloid peptide. This protein may have regulatory roles in cell death or proliferation signal cascades. Several alternatively spliced transcript variants of this gene are described but the full length nature of some variants has not been determined. Multiple polyadenylation sites have been found in this gene. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 24.1), ovary (RPKM 18.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TM2D3 in Genome Data Viewer
    Location:
    15q26.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (101632977..101652381, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (99378569..99410385, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (102173180..102192584, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene small nuclear ribonucleoprotein polypeptide C pseudogene 18 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr15:102119493-102120692 Neighboring gene long intergenic non-protein coding RNA 2348 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:102152533-102153033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:102153852-102154370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:102154371-102154887 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:102157328-102157940 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6891 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:102186842-102187008 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6892 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10195 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:102192988-102193878 Neighboring gene RNA, U6 small nuclear 807, pseudogene Neighboring gene threonyl-tRNA synthetase 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:102215750-102216274 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:102216275-102216797 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6894 Neighboring gene UBE2Q2 pseudogene 13

    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 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. Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease. Jakobsdottir J, et al. PLoS Genet, 2016 Oct. PMID 27764101, Free PMC Article
    2. TM2D3 rs675436 or FGFR2 rs755793 polymorphisms and susceptibility to Epstein-Barr virus-associated tumors in Chinese Han population. Zhang Q, et al. J Med Virol, 2018 Jun. PMID 29446487
    3. Cis- and trans-acting gene regulation is associated with osteoarthritis. Mahr S, et al. Am J Hum Genet, 2006 May. PMID 16642435, Free PMC Article
    4. beta -Amyloid peptide-induced apoptosis regulated by a novel protein containing a g protein activation module. Kajkowski EM, et al. J Biol Chem, 2001 Jun 1. PMID 11278849
    5. Mig-6 controls EGFR trafficking and suppresses gliomagenesis. Ying H, et al. Proc Natl Acad Sci U S A, 2010 Apr 13. PMID 20351267, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These findings indicated that the TT genotype and T allele frequencies of TM2D3 rs675436 were associated with an increased risk of Epstein-Barr virus-associated gastric carcinoma, while allele A or G of FGFR2 rs755793 had no effect on the occurrence of Epstein-Barr virus-associated tumors in Chinese Han population.
      Title: TM2D3 rs675436 or FGFR2 rs755793 polymorphisms and susceptibility to Epstein-Barr virus-associated tumors in Chinese Han population.
    2. Our results establish a rare TM2D3 variant in association with late-onset Alzheimer's disease susceptibility, and together with prior work suggests possible links to the beta-amyloid cascade
      Title: Rare Functional Variant in TM2D3 is Associated with Late-Onset Alzheimer's Disease.
    3. Our approach yielded 26 candidate genes differentially expressed between patients (Osteoarthritis) and controls. BLP2 and CIAS1 seem to be trans-regulated, as the absence of allelic expression imbalances suggests.
      Title: Cis- and trans-acting gene regulation is associated with osteoarthritis.
    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)

    Genotypes

    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

    Process Evidence Code Pubs
    involved_in lateral inhibition IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in lateral inhibition ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in positive regulation of Notch signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in plasma membrane ISM
    Inferred from Sequence Model
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    TM2 domain-containing protein 3
    Names
    BBP-like protein 2
    almondex homolog
    beta-amyloid-binding protein-like protein 2

    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_001307960.2 → NP_001294889.1  TM2 domain-containing protein 3 isoform c precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the 5' coding region and uses an alternate terminal exon compared to variant 1. The encoded isoform (c) is shorter and has a distinct C-terminus compared to isoform a.
      Source sequence(s)
      AC090164, AK297048
      Consensus CDS
      CCDS76795.1
      UniProtKB/TrEMBL
      B4DLL2, E7EPS7
      Related
      ENSP00000402179.2, ENST00000428002.6

    2. NM_001308026.2 → NP_001294955.1  TM2 domain-containing protein 3 isoform d precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate terminal exon compared to variant 1. The encoded isoform (d) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC090164, AK297048, BM984342, BU595412
      Consensus CDS
      CCDS76796.1
      UniProtKB/TrEMBL
      B4DLL2, H0YNS4
      Related
      ENSP00000454131.1, ENST00000559107.5

    3. NM_025141.4 → NP_079417.2  TM2 domain-containing protein 3 isoform b precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon within the coding region, but maintains the same reading frame, as compared to variant 1. Thus isoform b lacks an internal fragment of 26 aa compared to isoform a.
      Source sequence(s)
      AC090164, BQ272585
      Consensus CDS
      CCDS10392.1
      UniProtKB/TrEMBL
      B3KT51
      Related
      ENSP00000327584.3, ENST00000347970.7
      Conserved Domains (1) summary
      pfam05154
      Location:156 → 205
      TM2; TM2 domain

    4. NM_078474.3 → NP_510883.2  TM2 domain-containing protein 3 isoform a precursor

      See identical proteins and their annotated locations for NP_510883.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the full length isoform.
      Source sequence(s)
      AC090164, BC006150
      Consensus CDS
      CCDS10393.1
      UniProtKB/Swiss-Prot
      B2RDK9, Q9BRN9, Q9H046, Q9H651
      Related
      ENSP00000330433.3, ENST00000333202.8
      Conserved Domains (1) summary
      pfam05154
      Location:182 → 231
      TM2; TM2 domain

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      101632977..101652381 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      99378569..99410385 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008489017.1 RNA Sequence

    2. XR_008489016.1 RNA Sequence

    3. XR_008489015.1 RNA Sequence

    4. XR_008489014.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BRN9.2 GenPept UniProtKB/Swiss-Prot:Q9BRN9

    Gene LinkOut

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

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