RTN4RL2

reticulon 4 receptor like 2

Basic information

Region (hg38): 11:57460528-57477534

Links

ENSG00000186907 ∙ NCBI:349667 ∙ OMIM:610462 ∙ HGNC:23053 ∙ Uniprot:Q86UN3 ∙ 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 RTN4RL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN4RL2 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						0
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	0	0

Variants in RTN4RL2

This is a list of pathogenic ClinVar variants found in the RTN4RL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57467614-G-T		not specified	Uncertain significance (Feb 03, 2022)
11-57467618-C-T		not specified	Uncertain significance (Sep 16, 2021)
11-57467804-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-57468010-A-G		not specified	Uncertain significance (Sep 26, 2022)
11-57468019-G-A		not specified	Uncertain significance (Dec 01, 2022)
11-57476175-C-T		not specified	Uncertain significance (Mar 02, 2023)
11-57476177-G-A		not specified	Uncertain significance (Feb 27, 2024)
11-57476217-G-T		not specified	Uncertain significance (Aug 09, 2021)
11-57476327-A-T		not specified	Uncertain significance (Nov 30, 2021)
11-57476409-A-G		not specified	Uncertain significance (Jan 22, 2024)
11-57476457-G-A		not specified	Uncertain significance (Jan 24, 2024)
11-57476457-G-T		not specified	Uncertain significance (Oct 02, 2023)
11-57476480-C-A		not specified	Uncertain significance (Jun 23, 2023)
11-57476549-G-A		not specified	Uncertain significance (Apr 07, 2023)
11-57476594-A-C		not specified	Uncertain significance (Jun 18, 2021)
11-57476598-G-T		not specified	Uncertain significance (Jan 24, 2023)
11-57476675-G-T		not specified	Uncertain significance (Jun 29, 2023)
11-57476762-G-C		not specified	Uncertain significance (Apr 09, 2024)
11-57476775-G-A		not specified	Uncertain significance (Aug 01, 2022)
11-57476880-G-T		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RTN4RL2	protein_coding	protein_coding	ENST00000335099	3	16986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.877	0.123	122378	0	1	122379	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.47	114	216	0.527	0.0000120	2595
Missense in Polyphen		32	81.44	0.39293		944
Synonymous	0.947	98	111	0.885	0.00000607	967
Loss of Function	2.83	1	11.2	0.0892	5.74e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000547
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000547	0.0000547
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor that plays a functionally redundant role in the inhibition of neurite outgrowth mediated by MAG (By similarity). Plays a functionally redundant role in postnatal brain development. Contributes to normal axon migration across the brain midline and normal formation of the corpus callosum. Does not seem to play a significant role in regulating axon regeneration in the adult central nervous system. Protects motoneurons against apoptosis; protection against apoptosis is probably mediated by MAG (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:Q7M6Z0, ECO:0000250|UniProtKB:Q80WD1, 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

Haploinsufficiency Scores

• pHI: 0.282
• hipred: Y
• hipred_score: 0.715
• ghis: 0.510

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.254

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rtn4rl2
• Phenotype: normal 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); homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: rtn4rl2a
• Affected structure: posterior lateral line neuromast
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

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