RTN3
Basic information
Region (hg38): 11:63681446-63759891
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 3 | |||||
missense | 54 | 59 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 54 | 5 | 3 |
Variants in RTN3
This is a list of pathogenic ClinVar variants found in the RTN3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-63681641-C-T | not specified | Uncertain significance (Oct 12, 2022) | ||
11-63681666-C-T | Benign (Jul 11, 2018) | |||
11-63681680-C-T | not specified | Uncertain significance (Sep 28, 2022) | ||
11-63681700-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
11-63681740-C-G | not specified | Uncertain significance (Jun 10, 2024) | ||
11-63704885-A-C | Benign (Jun 01, 2018) | |||
11-63718920-G-A | not specified | Likely benign (Aug 02, 2021) | ||
11-63718954-T-A | not specified | Uncertain significance (Feb 02, 2024) | ||
11-63718965-C-T | not specified | Uncertain significance (Apr 04, 2023) | ||
11-63719179-A-T | not specified | Uncertain significance (Jan 27, 2022) | ||
11-63719278-A-G | not specified | Likely benign (May 26, 2024) | ||
11-63719346-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
11-63719365-C-T | not specified | Likely benign (Jul 14, 2023) | ||
11-63719394-A-G | not specified | Uncertain significance (Dec 17, 2021) | ||
11-63719410-G-C | not specified | Uncertain significance (Jan 04, 2024) | ||
11-63719421-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
11-63719423-G-A | not specified | Uncertain significance (Jan 30, 2024) | ||
11-63719424-T-C | not specified | Uncertain significance (Jan 23, 2024) | ||
11-63719454-A-G | not specified | Uncertain significance (Apr 26, 2023) | ||
11-63719508-A-G | not specified | Uncertain significance (May 15, 2024) | ||
11-63719513-C-T | Likely benign (Jan 01, 2023) | |||
11-63719598-G-A | not specified | Uncertain significance (May 28, 2024) | ||
11-63719646-A-G | not specified | Uncertain significance (May 28, 2024) | ||
11-63719650-C-T | not specified | Uncertain significance (Dec 27, 2023) | ||
11-63719763-G-C | not specified | Uncertain significance (Oct 05, 2021) |
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