RTN3

reticulon 3

Basic information

Region (hg38): 11:63681446-63759891

Links

ENSG00000133318 ∙ NCBI:10313 ∙ OMIM:604249 ∙ HGNC:10469 ∙ Uniprot:O95197 ∙ 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 RTN3 gene.

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.

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			75	9	1	85
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	75	10	3

Variants in RTN3

This is a list of pathogenic ClinVar variants found in the RTN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-63681641-C-T		not specified	Uncertain significance (Oct 12, 2022)
11-63681666-C-T			Benign (Jul 11, 2018)
11-63681680-C-T		not specified	Uncertain significance (Sep 28, 2022)
11-63681700-C-T		not specified	Uncertain significance (Apr 05, 2023)
11-63681740-C-G		not specified	Uncertain significance (Jun 10, 2024)
11-63704885-A-C			Benign (Jun 01, 2018)
11-63718819-A-G		not specified	Uncertain significance (Nov 11, 2024)
11-63718920-G-A		not specified	Likely benign (Aug 02, 2021)
11-63718954-T-A		not specified	Uncertain significance (Feb 02, 2024)
11-63718965-C-T		not specified	Uncertain significance (Apr 04, 2023)
11-63718974-A-G		not specified	Uncertain significance (Feb 25, 2025)
11-63719151-T-A		not specified	Uncertain significance (Jul 02, 2024)
11-63719166-G-A		not specified	Uncertain significance (Jan 01, 2025)
11-63719179-A-T		not specified	Uncertain significance (Jan 27, 2022)
11-63719187-T-C		not specified	Uncertain significance (Nov 25, 2024)
11-63719268-G-A		not specified	Uncertain significance (Jun 26, 2024)
11-63719278-A-G		not specified	Likely benign (May 26, 2024)
11-63719346-G-A		not specified	Uncertain significance (Nov 10, 2022)
11-63719365-C-T		not specified	Likely benign (Jul 14, 2023)
11-63719370-A-T		not specified	Likely benign (Jun 26, 2024)
11-63719394-A-G		not specified	Uncertain significance (Jan 27, 2025)
11-63719410-G-C		not specified	Uncertain significance (Jan 04, 2024)
11-63719412-C-T		not specified	Uncertain significance (Jun 26, 2024)
11-63719421-A-G		not specified	Uncertain significance (Jan 22, 2025)
11-63719423-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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

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