NUP155
protein-codingnucleoporin 155, the group of Nucleoporins
Gene summary
Nucleoporins are proteins that play an important role in the assembly and functioning of the nuclear pore complex (NPC) which regulates the movement of macromolecules across the nuclear envelope (NE). The protein encoded by this gene plays a role in the fusion of NE vesicles and formation of the double membrane NE. The protein may also be involved in cardiac physiology and may be associated with the pathogenesis of atrial fibrillation. Alternative splicing results in multiple transcript variants of this gene. A pseudogene associated with this gene is located on chromosome 6. [provided by RefSeq, May 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~83.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0018054
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014340
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0014340
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular
Intervention: Cardiovascular
Rationale: 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)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUP155 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_153485.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 29 | 4 | 37 | ||
| missense | 1 | 198 | 10 | 209 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 12 | 12 | ||||
| Total | 1 | 0 | 216 | 39 | 4 | 260 |
Highest pathogenic variant AF is 0.0000041055455
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_705618.1 | 35 | MANE Select | |
| Ensembl | ENSP00000231498.3 | 35 | MANE Select | |
| RefSeq | NP_001265241.1 | 34 | Standard | |
| RefSeq | NP_004289.1 | 34 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- tRNA processing
- Disease
- Gene expression (Transcription)
- Regulation of HSF1-mediated heat shock response
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
Molecular Function
- transporter activity
- protein binding
- structural constituent of nuclear pore
Cellular Component
- nuclear envelope
- membrane
- nuclear membrane
- nuclear pore inner ring
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000231498
- Coding exons
- 35
- Length
- 83045
- Individuals with no LoFs
- 125711
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 37
- Defined
- 125748
- p
- 0.000147
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.808 | 670 | 731 | 0.916 | 0.0000364 | 9118 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00038 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00016 | 0.00016 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- LoFtool
- 0.610
- RVIS EVS
- -1.9
- RVIS percentile EVS
- 1.96
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.823
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |