NUP54
nucleoporin 54, the group of Nucleoporins
Basic information
Region (hg38): 4:76107561-76148485
Links
Phenotypes
GenCC
Source:
- dystonia 37, early-onset, with striatal lesions (Limited), mode of inheritance: Unknown
- dystonia 37, early-onset, with striatal lesions (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Dystonia 37, early-onset, with striatal lesions | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 36333996 |
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 NUP54 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 | 15 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 17 | 1 | 0 |
Variants in NUP54
This is a list of pathogenic ClinVar variants found in the NUP54 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-76112398-T-C | not specified | Uncertain significance (Aug 17, 2021) | ||
| 4-76112494-C-A | not specified | Uncertain significance (Jan 23, 2023) | ||
| 4-76115380-C-T | not specified | Uncertain significance (Apr 22, 2022) | ||
| 4-76115470-G-A | - | no classification for the single variant (-) | ||
| 4-76115476-C-T | - | no classification for the single variant (-) | ||
| 4-76115477-CTGT-C | Dystonia 37, early-onset, with striatal lesions | Pathogenic (Jun 26, 2023) | ||
| 4-76124687-T-C | Dystonia 37, early-onset, with striatal lesions | Pathogenic (Jun 26, 2023) | ||
| 4-76124701-T-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 4-76124740-A-C | Dystonia 37, early-onset, with striatal lesions | Pathogenic (Jun 26, 2023) | ||
| 4-76124741-T-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 4-76130733-T-C | not specified | Uncertain significance (Feb 26, 2024) | ||
| 4-76132620-T-C | not specified | Uncertain significance (Jan 04, 2024) | ||
| 4-76132624-T-C | not specified | Uncertain significance (Mar 20, 2024) | ||
| 4-76132628-C-T | not specified | Likely benign (Jul 26, 2022) | ||
| 4-76134290-C-T | not specified | Uncertain significance (Oct 03, 2022) | ||
| 4-76134327-A-C | not specified | Uncertain significance (Oct 04, 2022) | ||
| 4-76136285-C-G | not specified | Uncertain significance (Mar 20, 2023) | ||
| 4-76144235-G-C | not specified | Uncertain significance (Oct 12, 2022) | ||
| 4-76144395-G-C | not specified | Uncertain significance (Feb 21, 2024) | ||
| 4-76144455-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
| 4-76148316-G-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 4-76148335-T-C | not specified | Uncertain significance (Jan 24, 2024) | ||
| 4-76148353-G-A | not specified | Uncertain significance (May 17, 2023) | ||
| 4-76148358-C-A | Dystonia 37, early-onset, with striatal lesions | Uncertain significance (Apr 04, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP54 | protein_coding | protein_coding | ENST00000264883 | 12 | 33857 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.216 | 0.784 | 125730 | 0 | 17 | 125747 | 0.0000676 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.14 | 161 | 258 | 0.624 | 0.0000123 | 3300 |
| Missense in Polyphen | 25 | 60.072 | 0.41617 | 837 | ||
| Synonymous | 1.41 | 76 | 93.3 | 0.815 | 0.00000469 | 987 |
| Loss of Function | 3.78 | 7 | 29.0 | 0.242 | 0.00000157 | 319 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000243 | 0.000239 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.0000536 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000163 | 0.000163 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the nuclear pore complex, a complex required for the trafficking across the nuclear membrane. {ECO:0000250|UniProtKB:P70582}.;
- 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
- 0.140
Intolerance Scores
- loftool
- 0.120
- rvis_EVS
- -0.2
- rvis_percentile_EVS
- 38.82
Haploinsufficiency Scores
- pHI
- 0.967
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.656
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.727
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nup54
- Phenotype
Zebrafish Information Network
- Gene name
- nup54
- Affected structure
- whole organism
- Phenotype tag
- abnormal
- Phenotype quality
- wholly ventralized
Gene ontology
- Biological process
- mRNA export from nucleus;protein targeting;NLS-bearing protein import into nucleus;nuclear pore organization;viral process;protein localization to nuclear inner membrane;regulation of protein import into nucleus;protein homooligomerization;protein heterotetramerization;protein heterotrimerization
- Cellular component
- nuclear envelope;nuclear membrane;nuclear pore central transport channel
- Molecular function
- protein binding;structural constituent of nuclear pore