NUP153
nucleoporin 153, the group of Zinc fingers RANBP2-type |Nucleoporins
Basic information
Region (hg38): 6:17615035-17706925
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 NUP153 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 | 6 | |||||
| missense | 78 | 10 | 91 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 78 | 12 | 8 |
Variants in NUP153
This is a list of pathogenic ClinVar variants found in the NUP153 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 6-17616133-A-C | Likely benign (Apr 01, 2022) | |||
| 6-17616164-A-G | not specified | Uncertain significance (Aug 28, 2023) | ||
| 6-17616174-C-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 6-17616599-G-A | not specified | Uncertain significance (Nov 07, 2023) | ||
| 6-17616615-C-T | not specified | Uncertain significance (Feb 05, 2024) | ||
| 6-17616656-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 6-17616690-C-G | not specified | Uncertain significance (Nov 09, 2024) | ||
| 6-17624573-T-C | Benign (Jun 15, 2018) | |||
| 6-17624618-C-T | not specified | Uncertain significance (Dec 17, 2023) | ||
| 6-17624620-G-A | not specified | Uncertain significance (Jun 07, 2024) | ||
| 6-17624624-G-A | not specified | Uncertain significance (Nov 27, 2024) | ||
| 6-17624717-C-A | not specified | Uncertain significance (Nov 09, 2023) | ||
| 6-17624725-T-C | not specified | Uncertain significance (Nov 08, 2024) | ||
| 6-17624770-T-C | not specified | Uncertain significance (Mar 13, 2023) | ||
| 6-17624773-G-A | not specified | Uncertain significance (Nov 28, 2024) | ||
| 6-17625826-T-C | not specified | Uncertain significance (Nov 08, 2021) | ||
| 6-17625841-C-T | not specified | Likely benign (Oct 01, 2024) | ||
| 6-17625858-G-A | not specified | Uncertain significance (Dec 14, 2023) | ||
| 6-17625861-T-C | not specified | Likely benign (Jan 26, 2023) | ||
| 6-17625876-C-T | not specified | Uncertain significance (Aug 12, 2021) | ||
| 6-17625935-G-C | not specified | Uncertain significance (Nov 12, 2021) | ||
| 6-17625981-G-A | not specified | Uncertain significance (Apr 09, 2024) | ||
| 6-17626006-C-T | not specified | Uncertain significance (Sep 14, 2023) | ||
| 6-17626050-T-C | not specified | Likely benign (Nov 08, 2021) | ||
| 6-17626076-T-C | not specified | Uncertain significance (May 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP153 | protein_coding | protein_coding | ENST00000262077 | 22 | 91388 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 9.89e-7 | 125740 | 0 | 7 | 125747 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.761 | 815 | 756 | 1.08 | 0.0000362 | 9528 |
| Missense in Polyphen | 207 | 233.63 | 0.88603 | 2959 | ||
| Synonymous | -1.78 | 316 | 278 | 1.14 | 0.0000139 | 3058 |
| Loss of Function | 6.62 | 5 | 60.6 | 0.0826 | 0.00000311 | 767 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000530 | 0.0000352 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.000217 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the nuclear pore complex (NPC), a complex required for the trafficking across the nuclear envelope. Functions as a scaffolding element in the nuclear phase of the NPC essential for normal nucleocytoplasmic transport of proteins and mRNAs. Involved in the quality control and retention of unspliced mRNAs in the nucleus; in association with TPR, regulates the nuclear export of unspliced mRNA species bearing constitutive transport element (CTE) in a NXF1- and KHDRBS1-independent manner. Mediates TPR anchoring to the nuclear membrane at NPC. The repeat- containing domain may be involved in anchoring other components of the NPC to the pore membrane. Possible DNA-binding subunit of the nuclear pore complex (NPC). {ECO:0000269|PubMed:12802065, ECO:0000269|PubMed:15229283, ECO:0000269|PubMed:22253824}.;
- Pathway
- RNA transport - Homo sapiens (human);TGF-Ncore;TGF-beta Signaling Pathway;tRNA processing;Disease;Gene expression (Transcription);sumoylation by ranbp2 regulates transcriptional repression;cycling of ran in nucleocytoplasmic transport;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;TGF_beta_Receptor;Transport of Mature mRNA derived from an Intron-Containing Transcript;mechanism of protein import into the nucleus;Signaling events mediated by HDAC Class II;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;Regulation of cytoplasmic and nuclear SMAD2/3 signaling;Sumoylation by RanBP2 regulates transcriptional repression;Transport of Mature Transcript to Cytoplasm;Signaling events mediated by HDAC Class I;Processing of Capped Intron-Containing Pre-mRNA;Arachidonic acid metabolism;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- loftool
- 0.0641
- rvis_EVS
- 0.84
- rvis_percentile_EVS
- 88.23
Haploinsufficiency Scores
- pHI
- 0.987
- hipred
- Y
- hipred_score
- 0.794
- ghis
- 0.605
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | High | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |
Mouse Genome Informatics
- Gene name
- Nup153
- Phenotype
Zebrafish Information Network
- Gene name
- nup153
- Affected structure
- intersegmental vessel
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- mRNA export from nucleus;protein import into nucleus;viral process;viral entry into host cell;negative regulation of RNA export from nucleus;nuclear pore complex assembly;viral penetration into host nucleus
- Cellular component
- nuclear pore;nucleoplasm;nucleolus;cytosol;nuclear membrane;nuclear periphery;nuclear inclusion body;host cell;nuclear pore central transport channel;nuclear pore nuclear basket
- Molecular function
- DNA binding;protein binding;nuclear localization sequence binding;structural constituent of nuclear pore;identical protein binding;protein membrane anchor;metal ion binding