NUP98

nucleoporin 98 and 96 precursor, the group of Nucleoporins

Basic information

Region (hg38): 11:3671082-3797792

Links

ENSG00000110713 ∙ NCBI:4928 ∙ OMIM:601021 ∙ HGNC:8068 ∙ Uniprot:P52948 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP98 gene.

• Inborn genetic diseases (54 variants)
• not provided (14 variants)

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				3	3	6
missense			51	4	5	60
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	51	7	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)
11-3676283-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)
11-3685998-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)
11-3693307-A-G			Likely benign (Dec 31, 2019)
11-3693342-C-T		not specified	Uncertain significance (Nov 22, 2023)
11-3695477-C-T		not specified	Uncertain significance (Feb 28, 2024)
11-3695492-T-G		not specified	Uncertain significance (Nov 06, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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