NUP42
protein-codingnucleoporin 42
Gene summary
Enables nuclear export signal receptor activity. Involved in protein export from nucleus. Located in nuclear membrane and nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]
- NUPL2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~19.2 kbGenCC 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 NUP42 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_007342.3. 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 | 1 | ||||
| missense | 69 | 3 | 72 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 0 | 74 | 3 | 0 | 77 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_031368.1 | 7 | MANE Select | |
| Ensembl | ENSP00000258742.5 | 7 | MANE Select | |
| RefSeq | NP_001357372.1 | 8 | Standard | |
| RefSeq | NP_001357373.1 | 7 | 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
- protein export from nucleus
- viral process
Molecular Function
- RNA binding
- nuclear export signal receptor activity
- protein binding
- metal ion binding
Cellular Component
- nucleus
- nuclear envelope
- nuclear pore
- nucleoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000258742
- Coding exons
- 7
- Length
- 19185
- Individuals with no LoFs
- 125682
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 66
- Defined
- 125748
- p
- 0.000262
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.00261 | 215 | 215 | 1.00 | 0.00000972 | 2734 |
| Missense (PolyPhen) | 54 | 60.2 | 0.89701 | 829 | ||
| Synonymous | 0.999 | 66 | 77.2 | 0.855 | 0.00000358 | 840 |
| Loss of Function | 0.682 | 14 | 17.0 | 0.822 | 7.18e-7 | 223 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00032 | 0.00029 | rare |
| South Asian | 0.00031 | 0.00029 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Required for the export of mRNAs containing poly(A) tails from the nucleus into the cytoplasm. In case of infection by HIV-1, it may participate in the docking of viral Vpr at the nuclear envelope. {ECO:0000269|PubMed:10610322, ECO:0000269|PubMed:16000379}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.840
- RVIS EVS
- 0.77
- RVIS percentile EVS
- 87.06
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |