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

Gene ID: 80213, updated on 5-Mar-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
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Genomic context

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Location:
15q26.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (101632977..101652381, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (99378569..99410385, complement)
105.20220307 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
  • 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 (16) 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_2023_10

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

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