NUP42
nucleoporin 42
Basic information
Region (hg38): 7:23181841-23201011
Previous symbols: [ "NUPL2" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP42 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 28 | 30 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 28 | 2 | 0 |
Variants in NUP42
This is a list of pathogenic ClinVar variants found in the NUP42 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-23182089-G-A | not specified | Likely benign (Oct 26, 2022) | ||
| 7-23182092-A-G | not specified | Uncertain significance (Feb 10, 2023) | ||
| 7-23182122-C-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 7-23182128-G-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 7-23182158-G-A | not specified | Uncertain significance (Aug 10, 2021) | ||
| 7-23182159-C-T | not specified | Uncertain significance (Jan 03, 2022) | ||
| 7-23185081-C-T | not specified | Uncertain significance (Dec 13, 2023) | ||
| 7-23185082-G-A | not specified | Uncertain significance (May 03, 2023) | ||
| 7-23185115-A-T | not specified | Uncertain significance (Nov 22, 2021) | ||
| 7-23185132-A-G | not specified | Uncertain significance (Mar 01, 2023) | ||
| 7-23185133-G-A | not specified | Uncertain significance (Jul 11, 2023) | ||
| 7-23185154-G-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 7-23185155-G-C | not specified | Uncertain significance (Apr 26, 2024) | ||
| 7-23185156-G-A | not specified | Uncertain significance (Nov 25, 2024) | ||
| 7-23185156-G-T | not specified | Uncertain significance (Oct 24, 2024) | ||
| 7-23185213-A-G | not specified | Uncertain significance (Jan 29, 2024) | ||
| 7-23185229-G-T | not specified | Uncertain significance (Oct 26, 2021) | ||
| 7-23185244-A-T | not specified | Uncertain significance (May 24, 2023) | ||
| 7-23187072-T-C | not specified | Uncertain significance (Dec 28, 2022) | ||
| 7-23196689-G-A | not specified | Likely benign (Jun 10, 2022) | ||
| 7-23196695-C-T | not specified | Uncertain significance (May 02, 2024) | ||
| 7-23196705-A-T | not specified | Uncertain significance (Dec 20, 2022) | ||
| 7-23199514-C-A | not specified | Uncertain significance (Oct 19, 2024) | ||
| 7-23200249-C-A | not specified | Uncertain significance (Aug 12, 2022) | ||
| 7-23200306-G-A | not specified | Uncertain significance (Jan 23, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP42 | protein_coding | protein_coding | ENST00000258742 | 7 | 19185 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 9.51e-9 | 0.309 | 125682 | 0 | 66 | 125748 | 0.000262 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.00261 | 215 | 215 | 1.00 | 0.00000972 | 2734 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000738 | 0.000738 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.000315 | 0.000290 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.000308 | 0.000294 |
| Other | 0.00 | 0.00 |
dbNSFP
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}.;
- Pathway
- RNA transport - Homo sapiens (human);tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Glycolysis and Gluconeogenesis;Infectious disease;Leukotriene metabolism;Squalene and cholesterol biosynthesis;Purine metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Vitamin B5 - CoA biosynthesis from pantothenate;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Phosphatidylinositol phosphate metabolism;Lysine metabolism;Methionine and cysteine metabolism;Selenoamino acid metabolism;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Aminosugars metabolism;Pentose phosphate pathway;Nuclear Pore Complex (NPC) Disassembly;De novo fatty acid biosynthesis;Glycerophospholipid metabolism;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Vitamin D3 (cholecalciferol) metabolism;Vitamin E metabolism;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Glycine, serine, alanine and threonine metabolism;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- loftool
- 0.840
- rvis_EVS
- 0.77
- rvis_percentile_EVS
- 87.06
Haploinsufficiency Scores
- pHI
- 0.154
- hipred
- N
- hipred_score
- 0.244
- ghis
- 0.501
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.987
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nupl2
- Phenotype
Gene ontology
- Biological process
- mRNA export from nucleus;protein export from nucleus;viral process
- Cellular component
- nucleus;nuclear envelope;nuclear pore;nucleoplasm;cytosol;nuclear membrane
- Molecular function
- RNA binding;nuclear export signal receptor activity;protein binding;metal ion binding