RTN4R
reticulon 4 receptor, the group of MicroRNA protein coding host genes
Basic information
Region (hg38): 22:20241415-20283246
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (74 variants)
- RTN4R-related_disorder (8 variants)
- Schizophrenia,_susceptibility_to (2 variants)
- Schizophrenia (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN4R gene is commonly pathogenic or not. These statistics are base on transcript: NM_000023004.6. 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 | 6 | |||||
| missense | 75 | 78 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 75 | 9 | 0 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RTN4R | protein_coding | protein_coding | ENST00000043402 | 2 | 41832 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.959 | 0.0411 | 119922 | 0 | 1 | 119923 | 0.00000417 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.13 | 265 | 322 | 0.822 | 0.0000239 | 2952 |
| Missense in Polyphen | 41 | 89.956 | 0.45578 | 979 | ||
| Synonymous | 0.129 | 146 | 148 | 0.986 | 0.0000106 | 1106 |
| Loss of Function | 2.93 | 0 | 9.97 | 0.00 | 5.19e-7 | 92 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000685 | 0.0000685 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Receptor for RTN4, OMG and MAG (PubMed:12037567, PubMed:12068310, PubMed:12426574, PubMed:12089450, PubMed:16712417, PubMed:18411262, PubMed:12839991, PubMed:19052207). Functions as receptor for the sialylated gangliosides GT1b and GM1 (PubMed:18411262). Besides, functions as receptor for chondroitin sulfate proteoglycans (By similarity). Can also bind heparin (By similarity). Intracellular signaling cascades are triggered via the coreceptor NGFR (PubMed:12426574). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:16712417, PubMed:22325200). Mediates axonal growth inhibition (PubMed:12839991, PubMed:19052207, PubMed:28892071). Plays a role in regulating axon regeneration and neuronal plasticity in the adult central nervous system. Plays a role in postnatal brain development. Required for normal axon migration across the brain midline and normal formation of the corpus callosum. Protects motoneurons against apoptosis; protection against apoptosis is probably mediated via interaction with MAG. Acts in conjunction with RTN4 and LINGO1 in regulating neuronal precursor cell motility during cortical development. Like other family members, plays a role in restricting the number dendritic spines and the number of synapses that are formed during brain development (PubMed:22325200). {ECO:0000250|UniProtKB:Q99PI8, ECO:0000269|PubMed:12037567, ECO:0000269|PubMed:12426574, ECO:0000269|PubMed:12839991, ECO:0000269|PubMed:14966521, ECO:0000269|PubMed:16712417, ECO:0000269|PubMed:18411262, ECO:0000269|PubMed:19052207, ECO:0000269|PubMed:28892071}.;
- Disease
- DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:15532024, ECO:0000269|PubMed:19052207, ECO:0000269|PubMed:28892071}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.;
- Pathway
- Spinal Cord Injury;p75(NTR)-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.216
Intolerance Scores
- loftool
- 0.197
- rvis_EVS
- -1.09
- rvis_percentile_EVS
- 7.05
Haploinsufficiency Scores
- pHI
- 0.233
- hipred
- Y
- hipred_score
- 0.586
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.950
Mouse Genome Informatics
- Gene name
- Rtn4r
- Phenotype
- cellular phenotype; homeostasis/metabolism 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Zebrafish Information Network
- Gene name
- rtn4r
- Affected structure
- cranial nerve
- Phenotype tag
- abnormal
- Phenotype quality
- morphology
Gene ontology
- Biological process
- cell surface receptor signaling pathway;axonogenesis;negative regulation of neuron projection development;corpus callosum development;neuronal signal transduction;negative regulation of axon extension;positive regulation of Rho protein signal transduction;positive regulation of GTPase activity;negative regulation of axon regeneration;negative regulation of axonogenesis
- Cellular component
- endoplasmic reticulum;plasma membrane;integral component of plasma membrane;cell surface;anchored component of external side of plasma membrane;neuron projection;neuronal cell body;dendritic shaft;perikaryon;axonal growth cone;membrane raft;extracellular exosome;presynapse;glutamatergic synapse
- Molecular function
- protein binding;heparin binding;chondroitin sulfate binding;signaling receptor activity;neuregulin receptor activity;ganglioside GM1 binding;ganglioside GT1b binding