NXF5
pseudonuclear RNA export factor 5
Gene summary
This gene is one member of a family of nuclear RNA export factor genes. Most transcript variants are candidates for nonsense-mediated decay (NMD) and may not express proteins in vivo. [provided by RefSeq, Sep 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
GenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Neurologic; Renal
Intervention: Cardiovascular
Rationale: In Familial heart block and focal segmental glomerulosclerosis, awareness of the risk of cardiac complications, including progressive heart block, may allow surveillance (eg, with electrocardiogram) and treatment (eg, with pacemaker placement); Renal transplant has been described
Comments: For Mental retardation, syndromic, X-linked, the evidence of variants as being related to disease causation has been questioned due to subsequent population-based studies
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NXF5 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript . 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 | 0 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| No transcripts match your selected source or search query. | ||||
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Influenza A - Homo sapiens (human)
- Ribosome biogenesis in eukaryotes - Homo sapiens (human)
- mRNA surveillance pathway - Homo sapiens (human)
- RNA transport - Homo sapiens (human)
- Herpes simplex infection - Homo sapiens (human)
Biological Process
- mRNA export from nucleus
- multicellular organism development
- poly(A)+ mRNA export from nucleus
- RNA transport
Molecular Function
- RNA binding
- protein binding
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000537026
- Coding exons
- 14
- Length
- 25465
- Individuals with no LoFs
- 125711
- Homozygous LoFs
- 9
- Heterozygous LoFs
- 26
- Defined
- 125746
- p
- 0.000139
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.374 | 141 | 129 | 1.09 | 0.0000100 | 2418 |
| Missense (PolyPhen) | 19 | 24.419 | 0.77807 | 579 | ||
| Synonymous | -1.16 | 61 | 50.5 | 1.21 | 0.00000395 | 645 |
| Loss of Function | -0.630 | 19 | 16.3 | 1.17 | 0.00000132 | 288 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0.00077 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000072 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000098 | 0.000070 | rare |
| South Asian | 0.00010 | 0.000065 | rare |
| Other | 0.00044 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Could be involved in the export of mRNA from the nucleus to the cytoplasm. Could also have a role in polarized cytoplasmic transport and localization of mRNA in neurons.;
- Disease
- DISEASE: Note=A chromosomal aberration involving NXF5 has been observed in one patient with a syndromic form of mental retardation and short stature. Pericentric inversion inv(X)(p21.1;q22) that interrupts NXF5. {ECO:0000269|PubMed:11566096}.;
Intolerance Scores
- LoFtool
- 0.720
- RVIS EVS
- 1.93
- RVIS percentile EVS
- 97.46
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |