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    NDC1 NDC1 transmembrane nucleoporin [ Homo sapiens (human) ]

    Gene ID: 55706, updated on 29-Oct-2024

    Summary

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    Official Symbol
    NDC1provided by HGNC
    Official Full Name
    NDC1 transmembrane nucleoporinprovided by HGNC
    Primary source
    HGNC:HGNC:25525
    See related
    Ensembl:ENSG00000058804 MIM:610115; AllianceGenome:HGNC:25525
    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
    NET3; TMEM48
    Summary
    A structural constituent of nuclear pore. Involved in nuclear pore complex assembly and nuclear pore localization. Located in actin cytoskeleton; nuclear membrane; and plasma membrane. Part of nuclear pore. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 8.4), colon (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See NDC1 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53765478..53838296, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53648324..53721147, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54231151..54303969, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene GLIS family zinc finger 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54159647-54160273 Neighboring gene RNA, U7 small nuclear 95 pseudogene Neighboring gene MPRA-validated peak235 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54181253-54181752 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54204253-54204971 Neighboring gene uncharacterized LOC124904179 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54236211-54236773 Neighboring gene small nucleolar RNA SNORA58 Neighboring gene uncharacterized LOC124904725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54277212-54277746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1050 Neighboring gene ribosomal protein L37 pseudogene 7 Neighboring gene Sharpr-MPRA regulatory region 6831 Neighboring gene Sharpr-MPRA regulatory region 3939 Neighboring gene Yip1 domain family member 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. TMEM48 promotes cell proliferation and invasion in cervical cancer via activation of the Wnt/β-catenin pathway. Jiang XY, et al. J Recept Signal Transduct Res, 2021 Aug. PMID 32896205
    2. Overexpression and biological function of TMEM48 in non-small cell lung carcinoma. Qiao W, et al. Tumour Biol, 2016 Feb. PMID 26392108
    3. NDC1 promotes hepatocellular carcinoma tumorigenesis by targeting BCAP31 to activate PI3K/AKT signaling. Liu YP, et al. J Biochem Mol Toxicol, 2024 Feb. PMID 38348718
    4. miRNA-mediated apoptosis activation through TMEM 48 inhibition in A549 cell line. Akkafa F, et al. Biochem Biophys Res Commun, 2018 Sep 3. PMID 29906465
    5. The transmembrane nucleoporin NDC1 is required for targeting of ALADIN to nuclear pore complexes. Yamazumi Y, et al. Biochem Biophys Res Commun, 2009 Nov 6. PMID 19703420

    See all (88) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic NDC1 variants that interfere with ALADIN binding are associated with neuropathy and triple A-like syndrome.
      Title: Biallelic NDC1 variants that interfere with ALADIN binding are associated with neuropathy and triple A-like syndrome.
    2. NDC1 promotes hepatocellular carcinoma tumorigenesis by targeting BCAP31 to activate PI3K/AKT signaling.
      Title: NDC1 promotes hepatocellular carcinoma tumorigenesis by targeting BCAP31 to activate PI3K/AKT signaling.
    3. TMEM48 promotes cell proliferation and invasion in cervical cancer via activation of the Wnt/beta-catenin pathway.
      Title: TMEM48 promotes cell proliferation and invasion in cervical cancer via activation of the Wnt/β-catenin pathway.
    4. miR-421 can suppress TMEM48 so that leads the non-small cancer cell lines (A549) to apoptosis.
      Title: miRNA-mediated apoptosis activation through TMEM 48 inhibition in A549 cell line.
    5. In mature human spermatozoa, SEPT12 and NDC1 are majorly colocalized in the centrosome regions; however, NDC1 is only slightly co-expressed with SEPT12 at the annulus of the sperm tail.
      Title: SEPT12-NDC1 Complexes Are Required for Mammalian Spermiogenesis.
    6. The biological relevance of TMEM48 in NSCLC progression.
      Title: Overexpression and biological function of TMEM48 in non-small cell lung carcinoma.
    7. ALADIN is anchored in the nuclear envelope via NDC1 and that this interaction gets lost, if ALADIN is mutated.
      Title: The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope.
    8. NDC1-mediated localization of ALADIN to nuclear pore complexes is essential for selective nuclear protein import; abrogation of the interaction between ALADIN and NDC1 may be important for the development of triple-A syndrome.
      Title: The transmembrane nucleoporin NDC1 is required for targeting of ALADIN to nuclear pore complexes.
    9. Human homologue NDC1/NET3 contains three FG repeats in the C-terminus, a feature of many nuclear pore proteins.
      Title: Topology of yeast Ndc1p: predictions for the human NDC1/NET3 homologue.
    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10407, FLJ12556, FLJ34120

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein-macromolecule adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables structural constituent of nuclear pore IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in homologous chromosome pairing at meiosis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in nuclear pore complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear pore localization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear pore organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in nucleocytoplasmic transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in protein transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in spermatogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in actin cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear envelope TAS
    Traceable Author Statement
    more info
    		  
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		  
    part_of nuclear pore IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of nuclear pore NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of nuclear pore transmembrane ring IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    nucleoporin NDC1
    Names
    nuclear division cycle 1 homolog
    transmembrane protein 48

    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_001168551.2 → NP_001162023.1  nucleoporin NDC1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AK295000, AL354612, BC003082
      UniProtKB/Swiss-Prot
      Q9BTX1
      Conserved Domains (1) summary
      pfam09531
      Location:20 → 626
      Ndc1_Nup; Nucleoporin protein Ndc1-Nup

    2. NM_018087.5 → NP_060557.3  nucleoporin NDC1 isoform 1

      See identical proteins and their annotated locations for NP_060557.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL049745, AL354612, BC003082
      Consensus CDS
      CCDS583.1
      UniProtKB/Swiss-Prot
      B4DHA3, B4DQQ5, G3XA81, Q8NB76, Q9BTX1, Q9H9T6, Q9NSG3, Q9NSG4, Q9NVZ7
      Related
      ENSP00000360483.3, ENST00000371429.4
      Conserved Domains (1) summary
      pfam09531
      Location:20 → 666
      Ndc1_Nup; Nucleoporin protein Ndc1-Nup

    RNA

    1. NR_033142.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK298909, AL354612, BC003082

    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
      53765478..53838296 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011541766.3 → XP_011540068.1  nucleoporin NDC1 isoform X1

      Conserved Domains (1) summary
      pfam09531
      Location:18 → 665
      Ndc1_Nup; Nucleoporin protein Ndc1-Nup

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      53648324..53721147 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054337564.1 → XP_054193539.1  nucleoporin NDC1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BTX1.2 GenPept UniProtKB/Swiss-Prot:Q9BTX1

    Gene LinkOut

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

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