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TMEM53 transmembrane protein 53 [ Homo sapiens (human) ]

Gene ID: 79639, updated on 2-Nov-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, Nov 2024]
Expression
Ubiquitous expression in liver (RPKM 3.6), testis (RPKM 3.6) and 25 other tissues See more
Orthologs
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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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

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

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