NXF3
protein-codingnuclear RNA export factor 3
Gene summary
This gene is one member of a family of nuclear RNA export factor genes. Common domain features of this family are a noncanonical RNP-type RNA-binding domain (RBD), 4 leucine-rich repeats (LRRs), a nuclear transport factor 2 (NTF2)-like domain that allows heterodimerization with NTF2-related export protein-1 (NXT1), and a ubiquitin-associated domain that mediates interactions with nucleoporins. The LRRs and NTF2-like domains are required for export activity. Alternative splicing seems to be a common mechanism in this gene family. The encoded protein of this gene has shortened LRR and ubiquitin-associated domains and its RDB is unable to bind RNA. It is located in the nucleoplasm but is not associated with either the nuclear envelope or the nucleolus. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.3 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 NXF3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022052.2. 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 | 6 | 6 | ||||
| missense | 51 | 8 | 59 | |||
| nonsense | 1 | 5 | 6 | |||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 10 | 10 | ||||
| Total | 0 | 1 | 72 | 8 | 0 | 81 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071335.1 | 19 | MANE Select | |
| Ensembl | ENSP00000378504.3 | 19 | MANE Select | |
| Ensembl | ENSP00000404017.1 | 15 | Standard | |
| Ensembl | ENSP00000811787.1 | 19 | Standard |
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
- poly(A)+ mRNA export from nucleus
Molecular Function
- RNA binding
- mRNA binding
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- nuclear RNA export factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000395065
- Coding exons
- 19
- Length
- 17420
- Individuals with no LoFs
- 125725
- Homozygous LoFs
- 6
- Heterozygous LoFs
- 14
- Defined
- 125745
- p
- 0.0000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.775 | 175 | 206 | 0.848 | 0.0000154 | 3557 |
| Missense (PolyPhen) | 28 | 40.096 | 0.69833 | 802 | ||
| Synonymous | 0.396 | 72 | 76.4 | 0.942 | 0.00000605 | 928 |
| Loss of Function | 3.04 | 8 | 24.1 | 0.332 | 0.00000167 | 417 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000076 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0011 | 0.00082 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000037 | 0.000026 | rare |
| South Asian | 0.000053 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as a tissue-specific nuclear mRNA export factor.;
Recessive Scores
- pRec
- 0.0854
Intolerance Scores
- LoFtool
- 0.572
- RVIS EVS
- -0.36
- RVIS percentile EVS
- 28.93
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.923
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |