RTN3

reticulon 3

Basic information

Region (hg38): 11:63681445-63759891

Links

ENSG00000133318

∙ NCBI:10313 ∙ OMIM:604249 ∙ HGNC:10469 ∙ Uniprot:O95197 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTN3 gene.

Inborn genetic diseases (30 variants)
not provided (3 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2	2
missense			29	1	1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding						0
Total	0	0	29	1	3

Variants in RTN3

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

Position	Phenotype	Significance	ClinVar
11-63681641-C-T	Inborn genetic diseases	Uncertain significance (Oct 12, 2022)	link
11-63681666-C-T		Benign (Jul 11, 2018)	link
11-63681680-C-T	Inborn genetic diseases	Uncertain significance (Sep 28, 2022)	link
11-63681700-C-T	Inborn genetic diseases	Uncertain significance (Apr 05, 2023)	link
11-63704885-A-C		Benign (Jun 01, 2018)	link
11-63718920-G-A	Inborn genetic diseases	Likely benign (Aug 02, 2021)	link
11-63718965-C-T	Inborn genetic diseases	Uncertain significance (Apr 04, 2023)	link
11-63719179-A-T	Inborn genetic diseases	Uncertain significance (Jan 27, 2022)	link
11-63719346-G-A	Inborn genetic diseases	Uncertain significance (Nov 10, 2022)	link
11-63719365-C-T	Inborn genetic diseases	Likely benign (Jul 14, 2023)	link
11-63719394-A-G	Inborn genetic diseases	Uncertain significance (Dec 17, 2021)	link
11-63719421-A-G	Inborn genetic diseases	Uncertain significance (Nov 10, 2022)	link
11-63719454-A-G	Inborn genetic diseases	Uncertain significance (Apr 26, 2023)	link
11-63719650-C-T	Inborn genetic diseases	Uncertain significance (Nov 30, 2021)	link
11-63719763-G-C	Inborn genetic diseases	Uncertain significance (Oct 05, 2021)	link
11-63719779-A-T	Inborn genetic diseases	Uncertain significance (Sep 22, 2022)	link
11-63719784-A-G	Inborn genetic diseases	Uncertain significance (Jun 28, 2022)	link
11-63719787-A-G	Inborn genetic diseases	Uncertain significance (Sep 14, 2022)	link
11-63719804-A-C	Inborn genetic diseases	Uncertain significance (Dec 16, 2022)	link
11-63719845-C-G	Inborn genetic diseases	Uncertain significance (Aug 16, 2021)	link
11-63719875-G-A	Inborn genetic diseases	Uncertain significance (Nov 17, 2022)	link
11-63719910-G-A	Inborn genetic diseases	Uncertain significance (Apr 24, 2023)	link
11-63720106-G-A	Inborn genetic diseases	Likely benign (Mar 17, 2023)	link
11-63720177-G-A	Inborn genetic diseases	Uncertain significance (Apr 18, 2023)	link
11-63720177-G-T	Inborn genetic diseases	Uncertain significance (Aug 21, 2023)	link

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
Phenotype

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