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GeneBe

RTN3

reticulon 3

Basic information

Region (hg38): 11:63681445-63759891

Links

ENSG00000133318NCBI:10313OMIM:604249HGNC:10469Uniprot:O95197AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (46 variants)
  • not provided (4 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.

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
clinvar
2
clinvar
3
missense
42
clinvar
4
clinvar
1
clinvar
47
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 42 5 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)2318261
11-63681666-C-T Benign (Jul 11, 2018)777228
11-63681680-C-T not specified Uncertain significance (Sep 28, 2022)2349268
11-63681700-C-T not specified Uncertain significance (Apr 05, 2023)2532949
11-63704885-A-C Benign (Jun 01, 2018)718662
11-63718920-G-A not specified Likely benign (Aug 02, 2021)2265333
11-63718954-T-A not specified Uncertain significance (Feb 02, 2024)3157023
11-63718965-C-T not specified Uncertain significance (Apr 04, 2023)2534308
11-63719179-A-T not specified Uncertain significance (Jan 27, 2022)2274177
11-63719346-G-A not specified Uncertain significance (Nov 10, 2022)2325306
11-63719365-C-T not specified Likely benign (Jul 14, 2023)2612194
11-63719394-A-G not specified Uncertain significance (Dec 17, 2021)2358199
11-63719410-G-C not specified Uncertain significance (Jan 04, 2024)3157024
11-63719421-A-G not specified Uncertain significance (Nov 10, 2022)2337316
11-63719423-G-A not specified Uncertain significance (Jan 30, 2024)3157025
11-63719424-T-C not specified Uncertain significance (Jan 23, 2024)3157026
11-63719454-A-G not specified Uncertain significance (Apr 26, 2023)2541110
11-63719513-C-T Likely benign (Jan 01, 2023)2641901
11-63719650-C-T not specified Uncertain significance (Dec 27, 2023)2315484
11-63719763-G-C not specified Uncertain significance (Oct 05, 2021)2386688
11-63719779-A-T not specified Uncertain significance (Sep 22, 2022)2312858
11-63719784-A-G not specified Uncertain significance (Jun 28, 2022)2298664
11-63719787-A-G not specified Uncertain significance (Sep 14, 2022)2213101
11-63719804-A-C not specified Uncertain significance (Dec 16, 2022)2336027
11-63719845-C-G not specified Uncertain significance (Aug 16, 2021)2382208

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