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NDC1 NDC1 transmembrane nucleoporin [ Homo sapiens (human) ]

Gene ID: 55706, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in lymph node (RPKM 8.4), colon (RPKM 6.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1p32.3
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53765478..53838296, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53648324..53721147, complement)
105.20220307 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
  • 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. 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
  4. 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
  5. The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope. Kind B, et al. Biochem Biophys Res Commun, 2009 Dec 11. PMID 19782045

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. The biological relevance of TMEM48 in NSCLC progression.
    Title: Overexpression and biological function of TMEM48 in non-small cell lung carcinoma.
  6. 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.
  7. 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.
  8. 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_2023_10

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

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