NUP153

Chr 6

nucleoporin 153

Also known as: HNUP153, N153

NCBI Gene: 9972ENSG00000124789UniProt: P49790

Nuclear pore complexes regulate the transport of macromolecules between the nucleus and cytoplasm. They are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. Nucleoporins are glycoproteins found in nuclear pores and contain characteristic pentapeptide XFXFG repeats as well as O-linked N-acetylglucosamine residues oriented towards the cytoplasm. The protein encoded by this gene has three distinct domains: a N-terminal region containing a pore targeting and an RNA-binding domain domain, a central region containing multiple zinc finger motifs, and a C-terminal region containing multiple XFXFG repeats. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

251
ClinVar variants
15
Pathogenic / LP
1.00
pLI score· haploinsufficient
0
Active trials
Clinical Summary— NUP153
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
15 Pathogenic / Likely Pathogenic· 209 VUS of 251 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
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.
0.17LOEUF
pLI 1.000
Z-score 6.62
OE 0.08 (0.04–0.17)
Highly constrained

Highly LoF-intolerant (top ~10% 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.
-0.76Z-score
OE missense 1.08 (1.02–1.14)
815 obs / 756.1 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.0.08 (0.04–0.17)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.08 (1.02–1.14)
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.1.14
0≤1.21.6
LoF obs/exp: 5 / 60.6Missense obs/exp: 815 / 756.1Syn Z: -1.78

ClinVar Variant Classifications

251 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic15
VUS209
Likely Benign19
Benign8
15
Pathogenic
209
VUS
19
Likely Benign
8
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
15
0
15
Likely Pathogenic
0
0
0
0
0
VUS
0
205
4
0
209
Likely Benign
0
17
0
2
19
Benign
0
3
1
4
8
Total0225206251

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

View in ClinVar →

Protein Context — Lollipop Plot

NUP153 · 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
The functional and clinical significance of nucleoporin NUP153 across human cancers: a systematic study based on multi-omics analysis and bench work validation.
He Y et al.·Front Immunol
2025Functional
NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15(INK4b).
Gan C et al.·Dig Liver Dis
2022
Capsid-host interactions for HIV-1 ingress.
Jang S et al.·Microbiol Mol Biol Rev
2023Review
Structural and mechanistic bases for resistance of the M66I capsid variant to lenacapavir.
Briganti L et al.·mBio
2025
Nuclear translocation of the LINE-1 encoded ORF1 protein alters nuclear envelope integrity in human neurons.
Znaidi R et al.·Brain Res
2025
Effect of Genetic Polymorphism Including NUP153 and SVEP1 on the Pharmacokinetics and Pharmacodynamics of Ticagrelor in Healthy Chinese Subjects.
Xiang Q et al.·Clin Drug Investig
2022
NUP153 overexpression suppresses the proliferation of colorectal cancer by negatively regulating Wnt/β-catenin signaling pathway and predicts good prognosis.
Wu Y et al.·Cancer Biomark
2019
Nuclear pore pathology underlying multisystem proteinopathy type 3-related inclusion body myopathy.
Izumi R et al.·Ann Clin Transl Neurol
2024
The nucleoporin Nup153 has separable roles in both early mitotic progression and the resolution of mitosis.
Mackay DR et al.·Mol Biol Cell
2009
Targeting and function in mRNA export of nuclear pore complex protein Nup153.
Bastos R et al.·J Cell Biol
1996
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