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GeneBe

RTN3

reticulon 3

Basic information

Region (hg38): 11:63681445-63759891

Links

ENSG00000133318NCBI:10313OMIM:604249HGNC:10469Uniprot:O95197AlphaFoldGenCCjaxSfariGnomADPubmed

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 Type 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

GeneTypeBio TypeTranscript Coding Exons Length
RTN3protein_codingprotein_codingENST00000377819 978446
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00006621.00125740081257480.0000318
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2395465301.030.00002546764
Missense in Polyphen120127.730.939481689
Synonymous-0.09232052031.010.00001032062
Loss of Function3.241333.10.3920.00000148472

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002890.0000289
Ashkenazi Jewish0.0003060.000298
East Asian0.000.00
Finnish0.00005480.0000462
European (Non-Finnish)0.00002690.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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