NXT2
protein-codingnuclear transport factor 2 like export factor 2
Gene summary
The protein encoded by this gene contains a nuclear transport factor 2 (NTF2) domain, which plays an important role in the trafficking of macromolecules, ions, and small molecules between the cytoplasm and nucleus. This protein may also have a role in mRNA nuclear export. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene. [provided by RefSeq, Jun 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NXT2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001242617.2. 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 | 3 | 3 | ||||
| missense | 15 | 1 | 16 | |||
| nonsense | 2 | 2 | ||||
| start loss | 1 | 1 | ||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 0 | 1 | 25 | 1 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001229546.1 | 4 | MANE Select | |
| Ensembl | ENSP00000361178.1 | 4 | MANE Select | |
| RefSeq | NP_001229547.1 | 3 | Standard | |
| RefSeq | NP_061168.2 | 5 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| nxt2 | Danio rerio | Structure: heart Quality: quality abnormal |
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)
Biological Process
- protein import into nucleus
- nucleocytoplasmic transport
- mRNA transport
Molecular Function
- protein binding
- protein transporter activity
Cellular Component
- nucleoplasm
- cytosol
- nuclear pore central transport channel
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000218004
- Coding exons
- 5
- Length
- 8910
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.12 | 41 | 66.8 | 0.614 | 0.00000456 | 1300 |
| Missense (PolyPhen) | 3 | 21.548 | 0.13923 | 437 | ||
| Synonymous | 0.135 | 23 | 23.8 | 0.965 | 0.00000153 | 362 |
| Loss of Function | 2.26 | 0 | 5.92 | 0.00 | 3.74e-7 | 120 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Regulator of protein export for NES-containing proteins. Also plays a role in mRNA nuclear export.;
Recessive Scores
- pRec
- 0.0289
Intolerance Scores
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.612
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Low | Low | Low |
| Cancer | Low | Low | Low |