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    TMEM53 transmembrane protein 53 [ Homo sapiens (human) ]

    Gene ID: 79639, updated on 28-Oct-2024

    Summary

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    Official Symbol
    TMEM53provided by HGNC
    Official Full Name
    transmembrane protein 53provided by HGNC
    Primary source
    HGNC:HGNC:26186
    See related
    Ensembl:ENSG00000126106 MIM:619722; AllianceGenome:HGNC:26186
    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
    CTDI; NET4
    Summary
    Involved in negative regulation of BMP signaling pathway; negative regulation of ossification; and regulation of nucleocytoplasmic transport. Located in nuclear membrane. Implicated in craniotubular dysplasia Ikegawa type. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in liver (RPKM 3.6), testis (RPKM 3.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM53 in Genome Data Viewer
    Location:
    1p34.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (44653247..44674481, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (44524186..44545427, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (45118919..45140153, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ring finger protein 220 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45011382-45011908 Neighboring gene microRNA 5584 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 810 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:45060915-45061086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45075197-45075758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45075759-45076318 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 939 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:45097341-45097888 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 941 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45098438-45098985 Neighboring gene uncharacterized LOC107984950 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:45115956-45116537 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 942 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:45139597-45140098 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 814 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 813 Neighboring gene uncharacterized LOC105378690 Neighboring gene small nucleolar RNA, C/D box 145 Neighboring gene armadillo like helical domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 815 Neighboring gene Sharpr-MPRA regulatory region 12667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 816 Neighboring gene RNA, U5F small nuclear 1 Neighboring gene RNA, U5D small nuclear 1

    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. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling. Guo L, et al. Nat Commun, 2021 Apr 6. PMID 33824347, Free PMC Article
    2. Nuclear membrane proteins with potential disease links found by subtractive proteomics. Schirmer EC, et al. Science, 2003 Sep 5. PMID 12958361
    3. FAM105A/OTULINL Is a Pseudodeubiquitinase of the OTU-Class that Localizes to the ER Membrane. Ceccarelli DF, et al. Structure, 2019 Jun 4. PMID 31056421, Free PMC Article
    4. Proteomic characterization of the human sperm nucleus. de Mateo S, et al. Proteomics, 2011 Jul. PMID 21630459
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling.
      Title: Deficiency of TMEM53 causes a previously unknown sclerosing bone disorder by dysregulation of BMP-SMAD signaling.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Craniotubular dysplasia, Ikegawa type
    MedGen: C5575335 OMIM: 619727 GeneReviews: Not available
    		not available

    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

    Clone Names

    • FLJ22353

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in negative regulation of BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of ossification IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of osteoblast differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of nucleocytoplasmic transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear outer membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus HDA PubMed 

    General protein information

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    Preferred Names
    transmembrane protein 53
    Names
    novel DUF829 domain-containing protein
    nuclear envelope transmembrane protein 4

    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_001300746.2 → NP_001287675.1  transmembrane protein 53 isoform 2

      See identical proteins and their annotated locations for NP_001287675.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate coding exon and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AL832539, BM675039, HY108001
      UniProtKB/Swiss-Prot
      Q6P2H8
      Related
      ENST00000476724.1
      Conserved Domains (1) summary
      pfam05705
      Location:13 → 198
      DUF829; Eukaryotic protein of unknown function (DUF829)

    2. NM_001300747.2 → NP_001287676.1  transmembrane protein 53 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (3) is shorter than isoform 1.
      Source sequence(s)
      BC064520, BM675039, HY029536, HY108001
      Consensus CDS
      CCDS72773.1
      UniProtKB/TrEMBL
      Q5TDE2
      Related
      ENSP00000361309.3, ENST00000372235.7
      Conserved Domains (1) summary
      pfam05705
      Location:36 → 241
      DUF829; Eukaryotic protein of unknown function (DUF829)

    3. NM_001300748.2 → NP_001287677.1  transmembrane protein 53 isoform 4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
      Source sequence(s)
      AA490195, BC064520, BM675039, HY108001
      UniProtKB/Swiss-Prot
      Q6P2H8
      Conserved Domains (1) summary
      pfam05705
      Location:36 → 240
      DUF829; Eukaryotic protein of unknown function (DUF829)

    4. NM_024587.4 → NP_078863.2  transmembrane protein 53 isoform 1

      See identical proteins and their annotated locations for NP_078863.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      BC064520, BM675039, HY108001
      Consensus CDS
      CCDS511.1
      UniProtKB/Swiss-Prot
      B4DKG0, Q5JPH2, Q6IA07, Q6P2H8, Q9H6E2
      Related
      ENSP00000361311.3, ENST00000372237.8
      Conserved Domains (1) summary
      pfam05705
      Location:36 → 271
      DUF829; Eukaryotic protein of unknown function (DUF829)

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      44653247..44674481 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      44524186..44545427 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6P2H8.1 GenPept UniProtKB/Swiss-Prot:Q6P2H8

    Gene LinkOut

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

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