NUP58

protein-coding

nucleoporin 58, the group of Nucleoporins

Gene summary

This gene encodes a member of the nucleoporin family that shares 87% sequence identity with rat nucleoporin p58. The protein is localized to the nuclear rim and is a component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

Previous symbols:

NUPL1

MANE transcript

NM_014089.4

Inheritance

—

ClinVar variants

U:82B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr13:25,301,524-25,365,390

External References & Databases

Ensembl (ENSG00000139496)

Transcript & Mutation Effects

hg38 • Region Span ~63.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUP58 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014089.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			78 clinvar	1 clinvar		79
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	82	1	1	84

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 60 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014089.4	RefSeq	NP_054808.1	16	MANE Select
ENST00000381736.8	Ensembl	ENSP00000371155.3	16	MANE Select
NM_001008564.2	RefSeq	NP_001008564.1	15	Standard
NM_001411001.1	RefSeq	NP_001397930.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

RNA transport - Homo sapiens (human)
tRNA processing
Disease
Gene expression (Transcription)
Regulation of HSF1-mediated heat shock response

Biological Process

mRNA export from nucleus
viral process
regulation of protein import into nucleus
protein homooligomerization
protein heterotetramerization

Molecular Function

protein binding
nuclear localization sequence binding
structural constituent of nuclear pore

Cellular Component

nuclear envelope
nuclear pore
nuclear membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000381736
Coding exons: 16
Length: 48277
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125741
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.06	254	306	0.830	0.0000140	3789
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00018	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000047	0.000046	rare
European (Non-Finnish)	0.000053	0.000053	rare
South Asian	0.000066	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane. {ECO:0000250|UniProtKB:P70581}.;

Recessive Scores

pRec: 0.0795

Intolerance Scores

RVIS EVS: -0.22
RVIS percentile EVS: 37.54

Essentials

Essential (gene trap): E