RTN3
reticulon 3
Basic information
Region (hg38): 11:63681445-63759891
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (30 variants)
- not provided (3 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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 2 | 2 | ||||
missense | 29 | 1 | 1 | 31 | ||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 29 | 1 | 3 |
Variants in RTN3
This is a list of pathogenic ClinVar variants found in the RTN3 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
11-63681641-C-T | Inborn genetic diseases | Uncertain significance (Oct 12, 2022) | ||
11-63681666-C-T | Benign (Jul 11, 2018) | |||
11-63681680-C-T | Inborn genetic diseases | Uncertain significance (Sep 28, 2022) | ||
11-63681700-C-T | Inborn genetic diseases | Uncertain significance (Apr 05, 2023) | ||
11-63704885-A-C | Benign (Jun 01, 2018) | |||
11-63718920-G-A | Inborn genetic diseases | Likely benign (Aug 02, 2021) | ||
11-63718965-C-T | Inborn genetic diseases | Uncertain significance (Apr 04, 2023) | ||
11-63719179-A-T | Inborn genetic diseases | Uncertain significance (Jan 27, 2022) | ||
11-63719346-G-A | Inborn genetic diseases | Uncertain significance (Nov 10, 2022) | ||
11-63719365-C-T | Inborn genetic diseases | Likely benign (Jul 14, 2023) | ||
11-63719394-A-G | Inborn genetic diseases | Uncertain significance (Dec 17, 2021) | ||
11-63719421-A-G | Inborn genetic diseases | Uncertain significance (Nov 10, 2022) | ||
11-63719454-A-G | Inborn genetic diseases | Uncertain significance (Apr 26, 2023) | ||
11-63719650-C-T | Inborn genetic diseases | Uncertain significance (Nov 30, 2021) | ||
11-63719763-G-C | Inborn genetic diseases | Uncertain significance (Oct 05, 2021) | ||
11-63719779-A-T | Inborn genetic diseases | Uncertain significance (Sep 22, 2022) | ||
11-63719784-A-G | Inborn genetic diseases | Uncertain significance (Jun 28, 2022) | ||
11-63719787-A-G | Inborn genetic diseases | Uncertain significance (Sep 14, 2022) | ||
11-63719804-A-C | Inborn genetic diseases | Uncertain significance (Dec 16, 2022) | ||
11-63719845-C-G | Inborn genetic diseases | Uncertain significance (Aug 16, 2021) | ||
11-63719875-G-A | Inborn genetic diseases | Uncertain significance (Nov 17, 2022) | ||
11-63719910-G-A | Inborn genetic diseases | Uncertain significance (Apr 24, 2023) | ||
11-63720106-G-A | Inborn genetic diseases | Likely benign (Mar 17, 2023) | ||
11-63720177-G-A | Inborn genetic diseases | Uncertain significance (Apr 18, 2023) | ||
11-63720177-G-T | Inborn genetic diseases | Uncertain significance (Aug 21, 2023) |
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