NUP54 nucleoporin 54 [Homo sapiens (human)] - Gene

Summary

Official Symbol: NUP54provided by HGNC
Official Full Name: nucleoporin 54provided by HGNC
Primary source: HGNC:HGNC:17359
See related: Ensembl:ENSG00000138750 MIM:607607; AllianceGenome:HGNC:17359
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DYT37
Summary: The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the phe-gly (FG) repeat-containing nucleoporin subset. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jun 2013]
Expression: Ubiquitous expression in bone marrow (RPKM 12.3), testis (RPKM 11.6) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 4q21.1

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (76114664..76148397, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (79455330..79489069, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (77035817..77069550, complement)

Chromosome 4 - NC_000004.12 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
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?

CircNUP54 promotes hepatocellular carcinoma progression via facilitating HuR cytoplasmic export and stabilizing BIRC3 mRNA.
Title: CircNUP54 promotes hepatocellular carcinoma progression via facilitating HuR cytoplasmic export and stabilizing BIRC3 mRNA.
Recessive NUP54 Variants Underlie Early-Onset Dystonia with Striatal Lesions.
Title: Recessive NUP54 Variants Underlie Early-Onset Dystonia with Striatal Lesions.
Data indicate a role for nucleoporin 54 (Nup54) in the response to ionising radiation (IR) and the maintenance of homologous recombination repair mediated genome integrity.
Title: Nucleoporin 54 contributes to homologous recombination repair and post-replicative DNA integrity.
Mutations within the footprinted region of Nup54 polymers blocked both polymerization and binding by the PRn poly-dipeptide. 1,6-hexanediol melted FG domain polymers in vitro and reversed PRn-mediated enhancement of the nuclear pore permeability barrier, suggesting that toxicity of the PRn poly-dipeptide results in part from its ability to lock the FG repeats of nuclear pore proteins in the polymerized state.
Title: Toxic PR(n) poly-dipeptides encoded by the C9orf72 repeat expansion block nuclear import and export.

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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
Dystonia 37, early-onset, with striatal lesions MedGen: C5830592 OMIM: 620427 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	HIV-1 Vpr binds to nucleoporin p54 in vitro during docking of the HIV-1 preintegration complex at the nuclear envelope	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RW13 (e-PCR)
- UniSTS:33028

NUP54 (e-PCR)
- UniSTS:33028

R71204 (e-PCR)
- UniSTS:33028

D1S1423 (e-PCR)
- UniSTS:149619

G54048 (e-PCR)
- UniSTS:109430

RH103869 (e-PCR)
- UniSTS:98194

RH93766 (e-PCR)
- UniSTS:89292

SHGC-78854 (e-PCR)
- UniSTS:95708

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IEA Inferred from Electronic Annotation more info
enables structural constituent of nuclear pore	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in NLS-bearing protein import into nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
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 localization to nuclear inner membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein targeting	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein import into nucleus	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
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	IEA Inferred from Electronic Annotation more info
part_of nuclear pore	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear pore central transport channel	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: nucleoporin p54

Names: 54 kDa nucleoporin; nucleoporin 54kD; nucleoporin 54kDa

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_001278603.2 → NP_001265532.1 nucleoporin p54 isoform 2

See identical proteins and their annotated locations for NP_001265532.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an in-frame exon in the 5' coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.

Source sequence(s)

AI580839, AK300036, BP420577

Consensus CDS

CCDS63998.1

UniProtKB/TrEMBL

Q53FD7

Related

ENSP00000421304.1, ENST00000514987.6

Conserved Domains (1) summary

pfam13874
Location:254 → 389

Nup54; Nucleoporin complex subunit 54
NM_017426.4 → NP_059122.2 nucleoporin p54 isoform 1

See identical proteins and their annotated locations for NP_059122.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AF157322, AI580839, BC012559, DA577078

Consensus CDS

CCDS3576.1

UniProtKB/Swiss-Prot

B2RCK7, B4DT35, Q7Z3B4, Q96EA7, Q9NVL5, Q9P0I1

UniProtKB/TrEMBL

Q53FD7

Related

ENSP00000264883.3, ENST00000264883.8

Conserved Domains (2) summary

pfam13874
Location:300 → 437

Nup54; Nucleoporin complex subunit 54

pfam18437
Location:453 → 491

Nup54_C; Nup54 C-terminal interacting domain

RNA

NR_103780.2 RNA Sequence

Status: REVIEWED

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 expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI580839, AK299442, BC012559, BC034226

Related

ENST00000695550.2
NR_103781.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks two internal exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF157322, AI580839, BC012559, BX538002

Related

ENST00000507257.6
NR_103782.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) has two additional exons in the 5' region and lacks two exons in a downstream region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AI580839, AK307571, BC012559, BC034226