RTN4RL1

reticulon 4 receptor like 1

Basic information

Region (hg38): 17:1934677-2025334

Links

ENSG00000185924 ∙ NCBI:146760 ∙ OMIM:610461 ∙ HGNC:21329 ∙ Uniprot:Q86UN2 ∙ 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 RTN4RL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN4RL1 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				1	2	3
missense			13		2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	4

Variants in RTN4RL1

This is a list of pathogenic ClinVar variants found in the RTN4RL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-1936546-C-T		not specified	Uncertain significance (Feb 27, 2024)
17-1936605-C-T		not specified	Uncertain significance (Jun 05, 2023)
17-1936638-G-A		not specified	Uncertain significance (Feb 27, 2023)
17-1936654-A-T		not specified	Uncertain significance (Oct 05, 2022)
17-1936669-G-T		not specified	Uncertain significance (Jan 19, 2024)
17-1936687-C-T		not specified	Uncertain significance (Jun 28, 2022)
17-1936748-G-T		not specified	Uncertain significance (Sep 27, 2021)
17-1936766-C-T			Benign (Feb 20, 2018)
17-1936767-G-A		not specified	Uncertain significance (Jun 09, 2022)
17-1936853-C-A		not specified	Uncertain significance (Dec 21, 2022)
17-1936899-G-A			Benign (Nov 20, 2017)
17-1936918-G-A		not specified	Uncertain significance (Mar 30, 2024)
17-1936932-C-T		not specified	Uncertain significance (Mar 16, 2024)
17-1936960-G-A		not specified	Uncertain significance (Jan 17, 2024)
17-1936988-G-A			Likely benign (May 01, 2022)
17-1937009-C-A		not specified	Uncertain significance (Apr 07, 2022)
17-1937034-G-A		not specified	Uncertain significance (Jun 30, 2022)
17-1937168-G-A			Benign (Feb 20, 2018)
17-1937383-C-T			Benign (Jan 05, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTN4RL1	protein_coding	protein_coding	ENST00000331238	2	90669

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.960	0.0397	124586	0	1	124587	0.00000401

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.47	212	281	0.753	0.0000190	2813
Missense in Polyphen		59	111.98	0.52686		1212
Synonymous	-0.509	148	140	1.05	0.0000106	940
Loss of Function	2.94	0	10.1	0.00	4.29e-7	119

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
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: Cell surface receptor. Plays a functionally redundant role in postnatal brain development and in regulating axon regeneration in the adult central nervous system. Contributes to normal axon migration across the brain midline and normal formation of the corpus callosum. Protects motoneurons against apoptosis; protection against apoptosis is probably mediated by MAG. Plays a role in inhibiting neurite outgrowth and axon regeneration via its binding to neuronal chondroitin sulfate proteoglycans. Binds heparin (By similarity). 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). Signaling mediates activation of Rho and downstream reorganization of the actin cytoskeleton (PubMed:22325200). {ECO:0000250|UniProtKB:Q8K0S5, ECO:0000269|PubMed:22325200}.
• Pathway: Post-translational modification: synthesis of GPI-anchored proteins;Post-translational protein modification;Metabolism of proteins (Consensus)

Recessive Scores

• pRec: 0.116

Intolerance Scores

• loftool: 0.0741
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.36

Haploinsufficiency Scores

• pHI: 0.544
• hipred: N
• hipred_score: 0.498
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.214

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rtn4rl1
• Phenotype: liver/biliary system 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); endocrine/exocrine gland phenotype

Gene ontology

• Biological process: negative regulation of neuron projection development;corpus callosum development;axon regeneration;negative regulation of axon regeneration
• Cellular component: extracellular region;extracellular space;plasma membrane;external side of plasma membrane;cell surface;extracellular matrix;cell projection;perikaryon;membrane raft;anchored component of plasma membrane;extracellular exosome
• Molecular function: protein binding;heparin binding;chondroitin sulfate binding;signaling receptor activity