NUP98
nucleoporin 98 and 96 precursor, the group of Nucleoporins
Basic information
Region (hg38): 11:3671083-3797792
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 NUP98 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 | 8 | |||||
| missense | 78 | 88 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | 2 | |||
| non coding | 0 | |||||
| Total | 0 | 0 | 78 | 10 | 8 |
Variants in NUP98
This is a list of pathogenic ClinVar variants found in the NUP98 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 11-3676173-C-T | not specified | Uncertain significance (Jul 26, 2022) | ||
| 11-3676184-C-T | not specified | Uncertain significance (Jan 24, 2024) | ||
| 11-3676209-G-A | not specified | Uncertain significance (May 11, 2022) | ||
| 11-3676221-T-C | not specified | Uncertain significance (May 26, 2024) | ||
| 11-3676247-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 11-3676283-C-T | not specified | Uncertain significance (Nov 10, 2022) | ||
| 11-3676333-A-G | Benign (Dec 28, 2017) | |||
| 11-3676347-G-A | not specified | Uncertain significance (Jan 10, 2023) | ||
| 11-3676355-T-C | Hirschsprung disease, susceptibility to, 1 | Likely pathogenic (Sep 27, 2016) | ||
| 11-3676364-C-T | Benign (Jan 05, 2018) | |||
| 11-3676513-C-G | not specified | Uncertain significance (Dec 08, 2023) | ||
| 11-3676560-G-A | not specified | Uncertain significance (Apr 28, 2022) | ||
| 11-3676587-G-T | not specified | Uncertain significance (Mar 07, 2024) | ||
| 11-3679564-T-C | not specified | Likely benign (Aug 02, 2022) | ||
| 11-3679582-A-G | not specified | Uncertain significance (Jun 12, 2023) | ||
| 11-3679586-T-C | not specified | Uncertain significance (Sep 06, 2022) | ||
| 11-3679613-A-G | not specified | Benign (-) | ||
| 11-3679685-C-T | not specified | Uncertain significance (Dec 12, 2023) | ||
| 11-3683214-C-T | Benign (Dec 31, 2019) | |||
| 11-3683293-T-C | not specified | Uncertain significance (Apr 09, 2024) | ||
| 11-3683406-C-T | not specified | Uncertain significance (Apr 08, 2024) | ||
| 11-3685998-C-T | not specified | Uncertain significance (Jun 12, 2023) | ||
| 11-3686180-T-C | not specified | Uncertain significance (May 26, 2022) | ||
| 11-3691425-C-T | not specified | Likely benign (Mar 01, 2024) | ||
| 11-3693260-G-A | Likely benign (Jun 08, 2018) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NUP98 | protein_coding | protein_coding | ENST00000324932 | 32 | 126710 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 6.31e-11 | 125737 | 0 | 9 | 125746 | 0.0000358 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.41 | 845 | 968 | 0.873 | 0.0000509 | 11690 |
| Missense in Polyphen | 347 | 464.65 | 0.7468 | 5774 | ||
| Synonymous | -0.216 | 351 | 346 | 1.01 | 0.0000168 | 3639 |
| Loss of Function | 8.11 | 5 | 86.4 | 0.0579 | 0.00000463 | 1018 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000904 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000531 | 0.0000527 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000356 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance. NUP98 and NUP96 are involved in the bidirectional transport across the NPC. May anchor NUP153 and TPR to the NPC. In cooperation with DHX9, plays a role in transcription and alternative splicing activation of a subset of genes (PubMed:28221134). Involved in the localization of DHX9 in discrete intranuclear foci (GLFG-body) (PubMed:28221134). {ECO:0000269|PubMed:15229283}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving NUP98 is found in a form of acute myeloid leukemia. Translocation t(7;11)(p15;p15) with HOXA9. Translocation t(11;17)(p15;p13) with PHF23. {ECO:0000269|PubMed:16028218}.; DISEASE: Note=A chromosomal aberration involving NUP98 is found in childhood acute myeloid leukemia. Translocation t(5;11)(q35;p15.5) with NSD1. Translocation t(8;11)(p11.2;p15) with WHSC1L1. {ECO:0000269|PubMed:16028218}.; DISEASE: Note=A chromosomal aberration involving NUP98 is found in a form of therapy-related myelodysplastic syndrome. Translocation t(11;20)(p15;q11) with TOP1. {ECO:0000269|PubMed:16028218}.; DISEASE: Note=A chromosomal aberration involving NUP98 is found in a form of T-cell acute lymphoblastic leukemia (T-ALL). Translocation t(3;11)(q12.2;p15.4) with LNP1. {ECO:0000269|PubMed:16028218}.; DISEASE: Note=A chromosomal aberration involving NUP98 is associated with pediatric acute myeloid leukemia (AML) with intermediate characteristics between M2-M3 French-American-British (FAB) subtypes. Translocation t(9;11)(p22;p15) with PSIP1/LEDGF. The chimeric transcript is an in-frame fusion of NUP98 exon 8 to PSIP1/LEDGF exon 4. {ECO:0000269|PubMed:16028218}.; DISEASE: Note=A chromosomal aberration involving NUP98 has been identified in acute leukemias. Translocation t(6;11)(q24.1;p15.5) with CCDC28A. The chimeric transcript is an in-frame fusion of NUP98 exon 13 to CCDC28A exon 2. Ectopic expression of NUP98- CCDC28A in mouse promotes the proliferative capacity and self- renewal potential of hematopoietic progenitors and rapidly induced fatal myeloproliferative neoplasms and defects in the differentiation of the erythro-megakaryocytic lineage. {ECO:0000269|PubMed:16028218}.;
- Pathway
- Influenza A - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Disease;Signal Transduction;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;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;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;RHO GTPases Activate Formins;Pyrimidine metabolism;SUMOylation;Glycosphingolipid metabolism;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;RHO GTPase Effectors;Phosphatidylinositol phosphate metabolism;Signaling by Rho GTPases;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;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Resolution of Sister Chromatid Cohesion;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
- 0.189
Intolerance Scores
- loftool
- 0.00393
- rvis_EVS
- -1.29
- rvis_percentile_EVS
- 5.01
Haploinsufficiency Scores
- pHI
- 0.934
- hipred
- Y
- hipred_score
- 0.697
- ghis
- 0.578
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.912
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nup98
- Phenotype
- growth/size/body region phenotype; hematopoietic system 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); embryo phenotype; immune system phenotype;
Zebrafish Information Network
- Gene name
- nup98
- Affected structure
- cerebellar central artery
- Phenotype tag
- abnormal
- Phenotype quality
- hemorrhagic
Gene ontology
- Biological process
- posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery;DNA replication;RNA export from nucleus;mRNA export from nucleus;proteolysis;protein import into nucleus;nucleocytoplasmic transport;nuclear pore organization;viral process;telomere tethering at nuclear periphery;positive regulation of mRNA splicing, via spliceosome;nuclear pore complex assembly;positive regulation of nucleic acid-templated transcription
- Cellular component
- kinetochore;nuclear envelope;nuclear pore;nucleoplasm;cytosol;nuclear body;nuclear pore outer ring;nuclear membrane;nuclear periphery;nuclear inclusion body;intracellular membrane-bounded organelle;nuclear pore cytoplasmic filaments;nuclear pore nuclear basket;ribonucleoprotein complex
- Molecular function
- transcription coactivator activity;RNA binding;mRNA binding;transporter activity;protein binding;nuclear localization sequence binding;serine-type peptidase activity;structural constituent of nuclear pore;promoter-specific chromatin binding