RTN3
Basic information
Region (hg38): 11:63681446-63759891
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (136 variants)
- not_provided (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001265589.2. 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 | 3 | |||||
missense | 125 | 11 | 137 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 125 | 12 | 3 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RTN3 | protein_coding | protein_coding | ENST00000377819 | 9 | 78446 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000662 | 1.00 | 125740 | 0 | 8 | 125748 | 0.0000318 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.239 | 546 | 530 | 1.03 | 0.0000254 | 6764 |
Missense in Polyphen | 120 | 127.73 | 0.93948 | 1689 | ||
Synonymous | -0.0923 | 205 | 203 | 1.01 | 0.0000103 | 2062 |
Loss of Function | 3.24 | 13 | 33.1 | 0.392 | 0.00000148 | 472 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000289 | 0.0000289 |
Ashkenazi Jewish | 0.000306 | 0.000298 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000548 | 0.0000462 |
European (Non-Finnish) | 0.0000269 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in membrane trafficking in the early secretory pathway. Inhibits BACE1 activity and amyloid precursor protein processing. May induce caspase-8 cascade and apoptosis. May favor BCL2 translocation to the mitochondria upon endoplasmic reticulum stress. In case of enteroviruses infection, RTN3 may be involved in the viral replication or pathogenesis. Induces the formation of endoplasmic reticulum tubules (PubMed:25612671). {ECO:0000269|PubMed:15286784, ECO:0000269|PubMed:16054885, ECO:0000269|PubMed:17031492, ECO:0000269|PubMed:17191123, ECO:0000269|PubMed:25612671}.;
- Pathway
- Alzheimer,s disease - Homo sapiens (human);Neuronal System;Synaptic adhesion-like molecules;Protein-protein interactions at synapses
(Consensus)
Recessive Scores
- pRec
- 0.0968
Intolerance Scores
- loftool
- 0.847
- rvis_EVS
- -0.84
- rvis_percentile_EVS
- 11.45
Haploinsufficiency Scores
- pHI
- 0.369
- hipred
- N
- hipred_score
- 0.301
- ghis
- 0.513
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.905
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rtn3
- Phenotype
Gene ontology
- Biological process
- apoptotic process;viral process;vesicle-mediated transport;endoplasmic reticulum tubular network organization;endoplasmic reticulum tubular network formation
- Cellular component
- Golgi membrane;extracellular space;endoplasmic reticulum;endoplasmic reticulum membrane;plasma membrane;integral component of membrane;synapse
- Molecular function
- protein binding