NTF3
neurotrophin 3, the group of Neurotrophins
Basic information
Region (hg38): 12:5432108-5521536
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (24 variants)
- not_provided (5 variants)
- Hirschsprung_disease,_susceptibility_to,_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTF3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001102654.2. 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 | 5 | |||||
| missense | 25 | 25 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 1 | 4 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| NTF3 | protein_coding | protein_coding | ENST00000423158 | 2 | 89425 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.932 | 0.0679 | 125744 | 0 | 3 | 125747 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.74 | 108 | 172 | 0.628 | 0.0000123 | 1736 |
| Missense in Polyphen | 40 | 86.146 | 0.46433 | 829 | ||
| Synonymous | 0.423 | 69 | 73.6 | 0.937 | 0.00000554 | 540 |
| Loss of Function | 3.08 | 1 | 13.0 | 0.0771 | 9.99e-7 | 114 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000621 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Seems to promote the survival of visceral and proprioceptive sensory neurons.;
- Pathway
- PI3K-Akt signaling pathway - Homo sapiens (human);Neurotrophin signaling pathway - Homo sapiens (human);Ras signaling pathway - Homo sapiens (human);MAPK signaling pathway - Homo sapiens (human);Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;MAPK Signaling Pathway;PI3K-Akt Signaling Pathway;Signal Transduction;role of erk5 in neuronal survival pathway;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;NTF3 activates NTRK2 (TRKB) signaling;Signaling by NTRK2 (TRKB);Signaling by NTRKs;BDNF;SHP2 signaling;GPCR signaling-G alpha i;Signaling by Receptor Tyrosine Kinases;Neurotrophic factor-mediated Trk receptor signaling;p75(NTR)-mediated signaling;Trk receptor signaling mediated by the MAPK pathway
(Consensus)
Recessive Scores
- pRec
- 0.530
Intolerance Scores
- loftool
- 0.448
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.12
Haploinsufficiency Scores
- pHI
- 0.352
- hipred
- Y
- hipred_score
- 0.786
- ghis
- 0.550
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.619
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ntf3
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; normal 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); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; muscle phenotype;
Gene ontology
- Biological process
- activation of MAPK activity;positive regulation of receptor internalization;signal transduction;transmembrane receptor protein tyrosine kinase signaling pathway;cell-cell signaling;nervous system development;peripheral nervous system development;memory;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of phospholipase C activity;positive regulation of phosphatidylinositol 3-kinase signaling;nerve development;positive regulation of cell migration;activation of protein kinase B activity;positive regulation of peptidyl-serine phosphorylation;nerve growth factor signaling pathway;regulation of apoptotic process;negative regulation of neuron apoptotic process;regulation of neuron differentiation;neuron projection morphogenesis;positive regulation of peptidyl-tyrosine phosphorylation;negative regulation of peptidyl-tyrosine phosphorylation;modulation of chemical synaptic transmission;positive chemotaxis;induction of positive chemotaxis;activation of GTPase activity;positive regulation of actin cytoskeleton reorganization
- Cellular component
- extracellular region;extracellular space;synaptic vesicle;axon;dendrite;cytoplasmic vesicle
- Molecular function
- signaling receptor binding;neurotrophin receptor binding;protein binding;growth factor activity;chemoattractant activity