NDC1 NDC1 transmembrane nucleoporin [Homo sapiens (human)] - Gene

Summary

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, Nov 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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
The biological relevance of TMEM48 in NSCLC progression.
Title: Overexpression and biological function of TMEM48 in non-small cell lung carcinoma.
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.
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.
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.

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Phenotypes

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-12414 (e-PCR)
- UniSTS:19502

SHGC-74855 (e-PCR)
- UniSTS:6713

REN31432 (e-PCR)
- UniSTS:356232

SHGC-74860 (e-PCR)
- UniSTS:52449

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 more info	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)

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
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

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

53765478..53838296 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011541766.3 → XP_011540068.1 nucleoporin NDC1 isoform X1

Conserved Domains (1) summary

pfam09531
Location:18 → 665

Ndc1_Nup; Nucleoporin protein Ndc1-Nup