NUP43

nucleoporin 43, the group of WD repeat domain containing|Nucleoporins

Basic information

Region (hg38): 6:149724315-149749665

Links

ENSG00000120253 ∙ NCBI:348995 ∙ OMIM:608141 ∙ HGNC:21182 ∙ Uniprot:Q8NFH3 ∙ 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 NUP43 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP43 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					1	1
missense			26	1	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	1	2

Variants in NUP43

This is a list of pathogenic ClinVar variants found in the NUP43 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-149727066-C-A		not specified	Uncertain significance (Mar 31, 2022)
6-149727070-T-G		not specified	Uncertain significance (Apr 23, 2024)
6-149727077-T-G		not specified	Uncertain significance (Jun 02, 2023)
6-149727109-G-C		not specified	Uncertain significance (Sep 16, 2021)
6-149727133-T-C		not specified	Uncertain significance (Mar 25, 2024)
6-149727145-G-A		not specified	Uncertain significance (Jun 17, 2024)
6-149727166-T-C		not specified	Uncertain significance (Aug 08, 2023)
6-149731629-C-T			Benign (Dec 31, 2019)
6-149731636-T-G		not specified	Uncertain significance (Jul 16, 2024)
6-149731646-C-T		not specified	Uncertain significance (Nov 11, 2024)
6-149731711-G-C		not specified	Uncertain significance (Aug 30, 2021)
6-149736483-G-A		not specified	Uncertain significance (May 01, 2024)
6-149736551-C-T		not specified	Uncertain significance (Jun 30, 2024)
6-149736587-C-T		not specified	Uncertain significance (Mar 16, 2022)
6-149742414-G-C		not specified	Uncertain significance (Oct 09, 2024)
6-149742476-C-T		not specified	Uncertain significance (Aug 08, 2022)
6-149742492-A-G		not specified	Uncertain significance (Apr 20, 2024)
6-149743691-C-T		not specified	Likely benign (Sep 03, 2024)
6-149745962-T-C		not specified	Uncertain significance (Aug 27, 2024)
6-149745974-T-C		not specified	Uncertain significance (Oct 12, 2024)
6-149745990-G-A			Benign (Mar 01, 2018)
6-149746015-G-C		not specified	Uncertain significance (Oct 25, 2024)
6-149746017-C-T		not specified	Uncertain significance (Oct 20, 2024)
6-149746389-G-C		not specified	Uncertain significance (Dec 07, 2023)
6-149746395-G-A		not specified	Uncertain significance (Dec 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP43	protein_coding	protein_coding	ENST00000340413	8	25351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000241	0.982	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.354	184	198	0.929	0.00000916	2497
Missense in Polyphen		25	40.021	0.62468		520
Synonymous	1.10	59	70.7	0.834	0.00000342	730
Loss of Function	2.12	11	21.7	0.507	0.00000123	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000190	0.000185
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000256	0.000255
Middle Eastern	0.00	0.00
South Asian	0.0000368	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the Nup107-160 subcomplex of the nuclear pore complex (NPC). The Nup107-160 subcomplex is required for the assembly of a functional NPC. The Nup107-160 subcomplex is also required for normal kinetochore microtubule attachment, mitotic progression and chromosome segregation. {ECO:0000269|PubMed:17363900}.
• Pathway: 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)

Intolerance Scores

• loftool: 0.852
• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.69

Haploinsufficiency Scores

• pHI: 0.485
• hipred: Y
• hipred_score: 0.552
• ghis: 0.657

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.716

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nup43

Zebrafish Information Network

• Gene name: nup43
• Affected structure: heart
• Phenotype tag: abnormal
• Phenotype quality: linear

Gene ontology

• Biological process: mRNA export from nucleus;cell cycle;chromosome segregation;viral process;cell division
• Cellular component: kinetochore;condensed chromosome kinetochore;nuclear envelope;cytosol;nuclear pore outer ring
• Molecular function: protein binding