NUP58

nucleoporin 58, the group of Nucleoporins

Basic information

Region (hg38): 13:25301524-25365390

Previous symbols: [ "NUPL1" ]

Links

ENSG00000139496 ∙ NCBI:9818 ∙ OMIM:607615 ∙ HGNC:20261 ∙ Uniprot:Q9BVL2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP58 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP58 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			36			36
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	0	1

Variants in NUP58

This is a list of pathogenic ClinVar variants found in the NUP58 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-25301859-C-T		not specified	Uncertain significance (Dec 30, 2024)
13-25301876-T-C		not specified	Uncertain significance (May 14, 2024)
13-25307811-C-A		not specified	Uncertain significance (Aug 21, 2023)
13-25307826-A-G		not specified	Uncertain significance (Jan 10, 2025)
13-25307844-G-A		not specified	Uncertain significance (Feb 12, 2024)
13-25307846-A-C		not specified	Uncertain significance (Dec 26, 2023)
13-25307873-C-G		not specified	Uncertain significance (Nov 09, 2023)
13-25307940-C-T		not specified	Uncertain significance (Nov 20, 2024)
13-25309253-C-T		not specified	Uncertain significance (Jun 29, 2022)
13-25309267-A-T		not specified	Uncertain significance (Jun 22, 2021)
13-25312912-A-G		not specified	Uncertain significance (Feb 13, 2024)
13-25312913-C-G		not specified	Uncertain significance (Jun 05, 2023)
13-25312948-T-A		not specified	Uncertain significance (Jun 07, 2024)
13-25313014-C-G		not specified	Uncertain significance (Mar 24, 2023)
13-25313018-C-G		not specified	Uncertain significance (Jul 26, 2023)
13-25313622-G-A		not specified	Uncertain significance (May 14, 2024)
13-25313649-A-T		not specified	Uncertain significance (Mar 03, 2025)
13-25313695-G-A		not specified	Uncertain significance (May 05, 2023)
13-25313698-C-A		not specified	Uncertain significance (Apr 18, 2023)
13-25313715-G-A		not specified	Uncertain significance (May 17, 2023)
13-25313725-T-G		not specified	Uncertain significance (Jul 11, 2023)
13-25313732-T-A		not specified	Uncertain significance (Jul 09, 2021)
13-25315405-C-A		not specified	Uncertain significance (Feb 23, 2023)
13-25319329-A-G		not specified	Uncertain significance (Feb 10, 2022)
13-25320532-A-C		not specified	Uncertain significance (Dec 28, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP58	protein_coding	protein_coding	ENST00000381736	16	48277

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.927	0.0730	125723	0	18	125741	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.06	254	306	0.830	0.0000140	3789
Missense in Polyphen		78	110.37	0.70672		1435
Synonymous	-0.723	125	115	1.09	0.00000594	1264
Loss of Function	4.27	5	30.4	0.165	0.00000137	384

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000300	0.000299
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000531	0.0000527
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000658	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane. {ECO:0000250|UniProtKB:P70581}.
• Pathway: RNA transport - Homo sapiens (human);tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Glycolysis and Gluconeogenesis;Infectious disease;Leukotriene metabolism;Squalene and cholesterol biosynthesis;Purine metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Vitamin B5 - CoA biosynthesis from pantothenate;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Phosphatidylinositol phosphate metabolism;Lysine metabolism;Methionine and cysteine metabolism;Selenoamino acid metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Pentose phosphate pathway;Nuclear Pore Complex (NPC) Disassembly;De novo fatty acid biosynthesis;Glycerophospholipid metabolism;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Vitamin D3 (cholecalciferol) metabolism;Vitamin E metabolism;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Glycine, serine, alanine and threonine metabolism;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA (Consensus)

Recessive Scores

• pRec: 0.0795

Intolerance Scores

• rvis_EVS: -0.22
• rvis_percentile_EVS: 37.54

Haploinsufficiency Scores

• pHI: 0.249
• hipred: Y
• hipred_score: 0.528
• ghis: 0.544

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Nupl1

Gene ontology

• Biological process: mRNA export from nucleus;viral process;regulation of protein import into nucleus;protein homooligomerization;protein heterotetramerization;protein heterotrimerization
• Cellular component: nuclear envelope;nuclear pore;nuclear membrane
• Molecular function: protein binding;nuclear localization sequence binding;structural constituent of nuclear pore