NUP155

nucleoporin 155, the group of Nucleoporins

Basic information

Region (hg38): 5:37288136-37371106

Links

ENSG00000113569

∙ NCBI:9631 ∙ OMIM:606694 ∙ HGNC:8063 ∙ Uniprot:O75694 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

atrial fibrillation, familial, 15 (Limited), mode of inheritance: AR
familial atrial fibrillation (Supportive), mode of inheritance: AD
atrial fibrillation, familial, 15 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Atrial fibrillation 15	AR	Cardiovascular	Though described individuals have suffered early morbidity and mortality despite early recognition and management, it is possible that preventive measures (including medical and surgical treatments) may be beneficial related cardiac arrthymias (atrial fibrillation)	Cardiovascular	15596564; 19070573

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NUP155 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUP155 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				6 clinvar	9 clinvar	15
missense			56 clinvar	2 clinvar		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	4	5
non coding					44 clinvar	44
Total	0	0	56	8	53

Variants in NUP155

This is a list of pathogenic ClinVar variants found in the NUP155 region.

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

Position	Phenotype	Significance	ClinVar
5-37291881-T-C		Benign (May 13, 2021)	1270364
5-37291950-T-C	not specified	Uncertain significance (Jan 31, 2024)	3203004
5-37292016-G-A	NUP155-related disorder	Likely benign (Apr 16, 2019)	3059048
5-37292030-A-C	not specified	Uncertain significance (Jan 19, 2024)	3203003
5-37292137-G-A		Benign (May 13, 2021)	1290619
5-37292217-ATT-A		Benign (May 13, 2021)	1267101
5-37292265-C-G		Benign (May 13, 2021)	1263135
5-37292885-C-T	not specified	Uncertain significance (Sep 13, 2023)	2623325
5-37293113-A-G		Benign (May 14, 2021)	1251251
5-37294294-G-T		Benign (May 13, 2021)	1247038
5-37294330-C-T	not specified	Uncertain significance (May 14, 2024)	3301470
5-37294341-C-A	not specified	Uncertain significance (Oct 21, 2021)	2256227
5-37294341-C-G	not specified	Uncertain significance (Dec 17, 2021)	3203002
5-37294371-T-C	NUP155-related disorder	Benign (May 04, 2021)	1294896
5-37294394-T-C	not specified	Uncertain significance (Feb 15, 2023)	2472868
5-37294457-C-T	not specified	Uncertain significance (Nov 13, 2023)	3203001
5-37298779-T-C		Benign (May 13, 2021)	1263247
5-37298883-G-A	not specified	Uncertain significance (Feb 05, 2024)	3203000
5-37298889-T-C	not specified	Uncertain significance (Jun 10, 2024)	3301468
5-37298893-A-G	NUP155-related disorder	Likely benign (Aug 01, 2019)	3035737
5-37298905-G-A		Benign (May 04, 2021)	776039
5-37298947-C-T		Benign (Dec 31, 2019)	767997
5-37298954-C-T	not specified	Uncertain significance (Jul 25, 2023)	2613840
5-37299474-G-A	not specified	Uncertain significance (Jan 05, 2022)	2270096
5-37299489-G-A	not specified	Uncertain significance (Jun 29, 2023)	2607633

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUP155	protein_coding	protein_coding	ENST00000231498	35	83045

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.653	0.347	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.808	670	731	0.916	0.0000364	9118
Missense in Polyphen		178	223.01	0.79818		2872
Synonymous	-0.950	273	254	1.08	0.0000129	2661
Loss of Function	6.59	18	82.6	0.218	0.00000433	965

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000376	0.000376
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Essential component of nuclear pore complex. Could be essessential for embryogenesis. Nucleoporins may be involved both in binding and translocating proteins during nucleocytoplasmic transport. {ECO:0000250|UniProtKB:Q99P88}.;
Disease: DISEASE: Atrial fibrillation, familial, 15 (ATFB15) [MIM:615770]: A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. {ECO:0000269|PubMed:19070573}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
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: 0.117

Intolerance Scores

loftool: 0.610
rvis_EVS: -1.9
rvis_percentile_EVS: 1.96

Haploinsufficiency Scores

pHI: 0.930
hipred: Y
hipred_score: 0.624
ghis: 0.659

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.823

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Nup155
Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery;mRNA export from nucleus;protein import into nucleus;nuclear envelope organization;viral process;protein localization to nuclear inner membrane;atrial cardiac muscle cell action potential
Cellular component: nuclear envelope;membrane;nuclear membrane;nuclear pore inner ring
Molecular function: transporter activity;protein binding;structural constituent of nuclear pore