NUP50

Chr 22

nucleoporin 50

Also known as: NPAP60, NPAP60L

NCBI Gene: 10762ENSG00000093000UniProt: Q9UKX7

The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a member of the FG-repeat containing nucleoporins that functions as a soluble cofactor in importin-alpha:beta-mediated nuclear protein import. Pseudogenes of this gene are found on chromosomes 5, 6, and 14. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

161
ClinVar variants
66
Pathogenic / LP
0.28
pLI score
0
Active trials
Clinical Summary— NUP50
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.24) despite low pLI — interpret in context.
📋
ClinVar Variants
66 Pathogenic / Likely Pathogenic· 76 VUS of 161 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.55LOEUF
pLI 0.283
Z-score 2.88
OE 0.24 (0.12–0.55)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
-0.07Z-score
OE missense 1.01 (0.92–1.12)
263 obs / 259.7 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.24 (0.12–0.55)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.01 (0.92–1.12)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.20
0≤1.21.6
LoF obs/exp: 4 / 16.7Missense obs/exp: 263 / 259.7Syn Z: -1.59

ClinVar Variant Classifications

161 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic65
Likely Pathogenic1
VUS76
Likely Benign2
Benign1
65
Pathogenic
1
Likely Pathogenic
76
VUS
2
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
65
0
65
Likely Pathogenic
0
0
1
0
1
VUS
0
71
5
0
76
Likely Benign
0
2
0
0
2
Benign
0
0
1
0
1
Total073720145

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NUP50 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
T cell and autoantibody recognition of nucleus-associated islet autoantigens in individuals with type 1 diabetes.
Guyer P et al.·Diabetologia
2025
Glycolysis-related genes predict prognosis and indicate immune microenvironment features in gastric cancer.
Xu L et al.·BMC Cancer
2024
TMEM160 Promotes Tumor Growth in Lung Adenocarcinoma and Cervical Adenocarcinoma Cell Lines.
Herrera-Quiterio GA et al.·Int J Mol Sci
2025
Novel minor HLA DR associated antigens in type 1 diabetes.
Müller D et al.·Clin Immunol
2018
Nuclear pore pathology underlying multisystem proteinopathy type 3-related inclusion body myopathy.
Izumi R et al.·Ann Clin Transl Neurol
2024
Integrated bioinformatic analysis of miR-15a/16-1 cluster network in cervical cancer.
S S et al.·Reprod Biol
2021
Identifying Novel Cell Glycolysis-Related Gene Signature Predictive of Overall Survival in Gastric Cancer.
Zhao X et al.·Biomed Res Int
2021
The role of vimentin in the tumor marker Nup88-dependent multinucleated phenotype.
Makise M et al.·BMC Cancer
2018
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools