NUP50
nucleoporin 50, the group of Nucleoporins
Basic information
Region (hg38): 22:45163925-45188017
Previous symbols: [ "NPAP60L" ]
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 NUP50 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 | 34 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 34 | 1 | 0 |
Variants in NUP50
This is a list of pathogenic ClinVar variants found in the NUP50 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-45171627-G-A | not specified | Uncertain significance (Apr 12, 2023) | ||
| 22-45171641-T-G | not specified | Uncertain significance (Sep 18, 2024) | ||
| 22-45171658-C-T | not specified | Uncertain significance (Mar 05, 2025) | ||
| 22-45171664-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
| 22-45175895-C-G | not specified | Uncertain significance (Nov 10, 2024) | ||
| 22-45175954-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
| 22-45175978-G-A | not specified | Uncertain significance (Aug 27, 2024) | ||
| 22-45176030-C-T | not specified | Uncertain significance (Aug 04, 2024) | ||
| 22-45176057-C-T | not specified | Likely benign (Jul 26, 2022) | ||
| 22-45176078-T-C | not specified | Uncertain significance (Jan 08, 2025) | ||
| 22-45178241-C-A | not specified | Uncertain significance (Dec 08, 2023) | ||
| 22-45178243-C-T | not specified | Uncertain significance (Feb 18, 2025) | ||
| 22-45178285-A-G | not specified | Uncertain significance (Jan 05, 2022) | ||
| 22-45178325-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
| 22-45178331-T-A | not specified | Uncertain significance (Jun 12, 2023) | ||
| 22-45178337-C-T | not specified | Uncertain significance (Jan 09, 2024) | ||
| 22-45178361-C-T | not specified | Uncertain significance (Jan 20, 2025) | ||
| 22-45178435-C-T | not specified | Uncertain significance (Jul 09, 2024) | ||
| 22-45178486-A-G | not specified | Uncertain significance (Feb 17, 2024) | ||
| 22-45178493-A-G | not specified | Uncertain significance (Jan 23, 2025) | ||
| 22-45178514-G-C | not specified | Uncertain significance (Oct 21, 2024) | ||
| 22-45178532-C-G | not specified | Uncertain significance (Feb 12, 2025) | ||
| 22-45178574-G-A | not specified | Uncertain significance (Jan 27, 2022) | ||
| 22-45178580-C-G | not specified | Uncertain significance (Jul 30, 2024) | ||
| 22-45178588-C-A | not specified | Uncertain significance (Nov 13, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP50 | protein_coding | protein_coding | ENST00000347635 | 7 | 24175 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.283 | 0.716 | 125730 | 0 | 18 | 125748 | 0.0000716 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0728 | 263 | 260 | 1.01 | 0.0000139 | 3071 |
| Missense in Polyphen | 51 | 78.675 | 0.64823 | 966 | ||
| Synonymous | -1.59 | 121 | 101 | 1.20 | 0.00000598 | 912 |
| Loss of Function | 2.88 | 4 | 16.7 | 0.239 | 7.81e-7 | 238 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000870 | 0.0000870 |
| Ashkenazi Jewish | 0.0000995 | 0.0000992 |
| East Asian | 0.000109 | 0.000109 |
| Finnish | 0.000139 | 0.000139 |
| European (Non-Finnish) | 0.0000617 | 0.0000615 |
| Middle Eastern | 0.000109 | 0.000109 |
| South Asian | 0.0000655 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the nuclear pore complex that has a direct role in nuclear protein import (PubMed:20016008). Actively displaces NLSs from importin-alpha, and facilitates disassembly of the importin-alpha:beta-cargo complex and importin recycling (PubMed:20016008). Interacts with regulatory proteins of cell cycle progression including CDKN1B (By similarity). This interaction is required for correct intracellular transport and degradation of CDKN1B (By similarity). {ECO:0000250|UniProtKB:Q9JIH2, ECO:0000269|PubMed:20016008}.;
- 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
- 0.120
Intolerance Scores
- loftool
- 0.247
- rvis_EVS
- -0.76
- rvis_percentile_EVS
- 13.33
Haploinsufficiency Scores
- pHI
- 0.926
- hipred
- Y
- hipred_score
- 0.693
- ghis
- 0.695
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.602
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nup50
- Phenotype
- nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); growth/size/body region phenotype;
Gene ontology
- Biological process
- mRNA export from nucleus;protein import into nucleus;viral process;positive regulation of GTPase activity
- Cellular component
- nucleus;nuclear pore;nucleoplasm;cytoplasm;nuclear membrane;intracellular membrane-bounded organelle
- Molecular function
- GTPase activator activity;protein binding;Ran GTPase binding