NXF5
Basic information
Region (hg38): X:101832537-101843278
Links
Phenotypes
GenCC
Source:
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Familial heart block and focal segmental glomerulosclerosis | XL | Cardiovascular | 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 | Cardiovascular; Neurologic; Renal | 11566096; 23686279; 23871722 |
| 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
This is a list of variants' phenotypes submitted to
- not provided (37 variants)
- Inborn genetic diseases (13 variants)
- Focal segmental glomerulosclerosis (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NXF5 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | |||||
| Total | 0 | 0 | 1 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NXF5 | protein_coding | protein_coding | ENST00000537026 | 14 | 25465 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 3.74e-14 | 0.00620 | 125711 | 9 | 26 | 125746 | 0.000139 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.374 | 141 | 129 | 1.09 | 0.0000100 | 2418 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000845 | 0.000830 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000722 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000977 | 0.0000703 |
| Middle Eastern | 0.0000722 | 0.0000544 |
| South Asian | 0.000105 | 0.0000653 |
| Other | 0.000445 | 0.000326 |
dbNSFP
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}.;
- Pathway
- 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)
(Consensus)
Intolerance Scores
- loftool
- 0.720
- rvis_EVS
- 1.93
- rvis_percentile_EVS
- 97.46
Haploinsufficiency Scores
- pHI
- 0.198
- hipred
- N
- hipred_score
- 0.158
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Nxf2
- Phenotype
- cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; 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);
Gene ontology
- Biological process
- mRNA export from nucleus;multicellular organism development;poly(A)+ mRNA export from nucleus;RNA transport
- Cellular component
- nucleus;cytoplasm
- Molecular function
- RNA binding;protein binding