RTN4R

reticulon 4 receptor, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 22:20241415-20283246

Links

ENSG00000040608 ∙ NCBI:65078 ∙ OMIM:605566 ∙ HGNC:18601 ∙ Uniprot:Q9BZR6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTN4R gene.

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.

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				6		6
missense			31	3		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	9	0

Variants in RTN4R

This is a list of pathogenic ClinVar variants found in the RTN4R region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-20241725-G-A		not specified	Uncertain significance (Apr 27, 2022)
22-20241735-C-T		RTN4R-related disorder	Likely benign (Dec 16, 2019)
22-20241740-C-T		not specified	Uncertain significance (Oct 10, 2023)
22-20241757-G-C		not specified	Uncertain significance (Nov 14, 2023)
22-20241760-G-A		not specified	Uncertain significance (Feb 12, 2024)
22-20241768-G-A		RTN4R-related disorder	Likely benign (May 01, 2019)
22-20241815-C-T		not specified	Uncertain significance (Jun 29, 2022)
22-20241832-G-T		not specified	Uncertain significance (Dec 19, 2022)
22-20241834-C-G		not specified	Uncertain significance (Dec 03, 2021)
22-20241926-A-G		not specified	Uncertain significance (Feb 28, 2023)
22-20241994-T-C		not specified	Uncertain significance (Aug 02, 2021)
22-20242003-C-T		Schizophrenia	Uncertain significance (Mar 29, 2024)
22-20242016-C-T		not specified	Uncertain significance (Sep 27, 2021)
22-20242017-G-A		RTN4R-related disorder	Likely benign (Mar 03, 2020)
22-20242046-C-T		RTN4R-related disorder	Likely benign (Nov 04, 2019)
22-20242047-G-A		RTN4R-related disorder	Likely benign (Feb 20, 2019)
22-20242067-C-T		not specified	Uncertain significance (Apr 27, 2022)
22-20242118-C-T		not specified	Uncertain significance (Apr 01, 2024)
22-20242201-A-G		not specified	Uncertain significance (Jan 04, 2022)
22-20242228-G-C		not specified	Uncertain significance (Dec 06, 2022)
22-20242246-C-T		not specified	Uncertain significance (Jun 27, 2023)
22-20242282-T-A		not specified	Uncertain significance (Dec 19, 2022)
22-20242297-C-T		not specified	Uncertain significance (Oct 05, 2022)
22-20242324-G-T		not specified	Uncertain significance (Jan 03, 2024)
22-20242385-G-A		not specified	Uncertain significance (May 26, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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