NUP88

nucleoporin 88, the group of Nucleoporins

Basic information

Region (hg38): 17:5359667-5420164

Links

ENSG00000108559 ∙ NCBI:4927 ∙ OMIM:602552 ∙ HGNC:8067 ∙ Uniprot:Q99567 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• fetal akinesia deformation sequence 4 (Strong), mode of inheritance: AR
• fetal akinesia deformation sequence 1 (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Fetal akinesia deformation sequence 4	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	Musculoskeletal; Neurologic	30543681

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP88 gene.

• Inborn genetic diseases (36 variants)
• Fetal akinesia deformation sequence 4 (12 variants)
• not provided (7 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP88 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	1	3	7
missense			30	2	1	33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			7	2	5	14
Total	0	0	40	5	9

Variants in NUP88

This is a list of pathogenic ClinVar variants found in the NUP88 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-5361214-T-G		not specified	Uncertain significance (Feb 27, 2024)
17-5361291-G-A			Likely benign (May 01, 2022)
17-5361318-C-T			Likely benign (Oct 17, 2017)
17-5361473-C-T		not specified	Uncertain significance (Nov 23, 2022)
17-5361511-A-T		not specified	Uncertain significance (Dec 19, 2023)
17-5362953-G-A		not specified	Uncertain significance (Jun 07, 2023)
17-5365201-A-G		not specified	Uncertain significance (May 17, 2023)
17-5365221-G-A		Teratoma	Uncertain significance (Jan 01, 2023)
17-5365235-C-A		not specified	Uncertain significance (Apr 18, 2023)
17-5368374-C-G		not specified	Uncertain significance (Sep 20, 2023)
17-5368377-C-T		not specified	Uncertain significance (Dec 17, 2023)
17-5368382-G-A		not specified	Uncertain significance (May 06, 2022)
17-5368455-T-C		not specified	Uncertain significance (Sep 20, 2023)
17-5373408-T-G		not specified	Uncertain significance (Aug 17, 2022)
17-5373449-A-G		not specified	Uncertain significance (Sep 27, 2021)
17-5377170-G-A		not specified	Uncertain significance (Apr 13, 2023)
17-5377182-G-A		not specified	Uncertain significance (Jan 16, 2024)
17-5380401-A-T		not specified	Uncertain significance (Nov 21, 2023)
17-5381385-T-C			Benign (Oct 17, 2017)
17-5383168-G-A		not specified	Uncertain significance (Mar 14, 2023)
17-5386213-T-A		not specified	Uncertain significance (May 18, 2023)
17-5386234-T-C		NUP88-related disorder	Benign (Jul 01, 2022)
17-5386260-A-G		Fetal akinesia deformation sequence 4	Benign (Sep 05, 2021)
17-5386713-T-C		Fetal akinesia deformation sequence 4	Benign (Sep 05, 2021)
17-5386738-C-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP88	protein_coding	protein_coding	ENST00000573584	17	59223

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.96e-8	1.00	125641	0	107	125748	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.526	436	406	1.07	0.0000208	4821
Missense in Polyphen		134	132.61	1.0105		1623
Synonymous	-0.231	161	157	1.02	0.00000832	1432
Loss of Function	3.18	20	42.3	0.473	0.00000223	510

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000510	0.000509
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000493	0.000489
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000521	0.000519
Middle Eastern	0.000493	0.000489
South Asian	0.000559	0.000555
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential component of nuclear pore complex.
• 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: 0.103

Intolerance Scores

• loftool: 0.887
• rvis_EVS: -1.11
• rvis_percentile_EVS: 6.86

Haploinsufficiency Scores

• pHI: 0.908
• hipred: Y
• hipred_score: 0.590
• ghis: 0.626

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.588

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nup88

Zebrafish Information Network

• Gene name: nup88
• Affected structure: melanocyte
• Phenotype tag: abnormal
• Phenotype quality: quality

Gene ontology

• Biological process: ribosomal large subunit export from nucleus;ribosomal small subunit export from nucleus;mitotic cell cycle;mRNA export from nucleus;protein import into nucleus;protein export from nucleus;viral process
• Cellular component: nuclear pore;nucleoplasm;cytosol
• Molecular function: transporter activity;structural constituent of nuclear pore