NUP42

Chr 7

nucleoporin 42

Also known as: CG1, NLP-1, NLP1, NLP_1, NUPL2, UIP1, hCG1

NCBI Gene: 11097ENSG00000136243UniProt: O15504

Enables nuclear export signal receptor activity. Involved in protein export from nucleus. Located in cytosol; nuclear membrane; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

107
ClinVar variants
31
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NUP42
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
31 Pathogenic / Likely Pathogenic· 72 VUS of 107 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
1.28LOEUF
pLI 0.000
Z-score 0.68
OE 0.82 (0.54–1.28)
Tolerant

Highly tolerant — LoF variants common in population

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.
-0.00Z-score
OE missense 1.00 (0.89–1.12)
215 obs / 214.9 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.0.82 (0.54–1.28)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.00 (0.89–1.12)
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.0.86
0≤1.21.6
LoF obs/exp: 14 / 17.0Missense obs/exp: 215 / 214.9Syn Z: 1.00

ClinVar Variant Classifications

107 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic29
Likely Pathogenic2
VUS72
Likely Benign4
29
Pathogenic
2
Likely Pathogenic
72
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
29
0
29
Likely Pathogenic
0
0
2
0
2
VUS
0
67
5
0
72
Likely Benign
0
3
1
0
4
Benign
0
0
0
0
0
Total070370107

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

View in ClinVar →

Protein Context — Lollipop Plot

NUP42 · 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
NUCLEOPORIN 42; NUP42
MIM #619998 · *
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Structural and functional analysis of mRNA export regulation by the nuclear pore complex.
Lin DH et al.·Nat Commun
2018Functional
Coronavirus nucleocapsid protein enhances the binding of p-PKCα to RACK1: Implications for inhibition of nucleocytoplasmic trafficking and suppression of the innate immune response.
Xue W et al.·PLoS Pathog
2024
Nup42 and IP(6) coordinate Gle1 stimulation of Dbp5/DDX19B for mRNA export in yeast and human cells.
Adams RL et al.·Traffic
2017
Mendelian Randomization Study Using Dopaminergic Neuron-Specific eQTL Nominates Potential Causal Genes for Parkinson's Disease.
Dang X et al.·Mov Disord
2022
Putative reaction intermediates in Crm1-mediated nuclear protein export.
Floer M et al.·J Biol Chem
1999
Rad51 Paralogs Remodel Pre-synaptic Rad51 Filaments to Stimulate Homologous Recombination.
Taylor MRG et al.·Cell
2015Functional
A new nucleoporin-like protein interacts with both HIV-1 Rev nuclear export signal and CRM-1.
Farjot G et al.·J Biol Chem
1999
Docking of HIV-1 Vpr to the nuclear envelope is mediated by the interaction with the nucleoporin hCG1.
Le Rouzic E et al.·J Biol Chem
2002
The nucleoporin-like protein NLP1 (hCG1) promotes CRM1-dependent nuclear protein export.
Waldmann I et al.·J Cell Sci
2012
Herpesvirus capsid association with the nuclear pore complex and viral DNA release involve the nucleoporin CAN/Nup214 and the capsid protein pUL25.
Pasdeloup D et al.·J Virol
2009
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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