Menu
GeneBe

RTN1

reticulon 1, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 14:59595975-59870776

Previous symbols: [ "NSP" ]

Links

ENSG00000139970NCBI:6252OMIM:600865HGNC:10467Uniprot:Q16799AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RTN1 gene.

  • not provided (7 variants)
  • Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RTN1 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
2
clinvar
2
missense
4
clinvar
1
clinvar
4
clinvar
9
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
1
clinvar
1
Total 0 0 4 1 7

Variants in RTN1

This is a list of pathogenic ClinVar variants found in the RTN1 region.

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

Position Type Phenotype Significance ClinVar
14-59603075-C-T Inborn genetic diseases Uncertain significance (Jan 03, 2022)2268867
14-59727466-C-T Benign (Jul 13, 2018)787944
14-59727615-T-C Benign (Jul 26, 2018)781130
14-59727639-C-A Inborn genetic diseases Likely benign (Jul 20, 2021)2316510
14-59745747-C-A Inborn genetic diseases Uncertain significance (Oct 05, 2021)2262533
14-59745807-T-G Inborn genetic diseases Uncertain significance (Aug 09, 2021)2372374
14-59745908-C-T Benign (Jul 15, 2018)708579
14-59745983-C-T Benign (Dec 31, 2019)781131
14-59746084-G-A Benign (Jul 23, 2018)778741
14-59746353-T-C Benign (Jul 23, 2018)778742
14-59746427-T-C Inborn genetic diseases Uncertain significance (Sep 01, 2021)2248086
14-59746490-C-G Benign (Jul 23, 2018)790143

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RTN1protein_codingprotein_codingENST00000267484 9274991
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9860.0141125697061257030.0000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.9503664210.8700.00002474911
Missense in Polyphen80130.350.613711591
Synonymous0.03811921930.9970.00001381629
Loss of Function4.19326.10.1150.00000111357

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001240.000123
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.00002730.0000264
Middle Eastern0.000.00
South Asian0.000.00
Other0.0001680.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: May be involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells.;

Recessive Scores

pRec
0.118

Intolerance Scores

loftool
0.217
rvis_EVS
0.13
rvis_percentile_EVS
63.57

Haploinsufficiency Scores

pHI
0.507
hipred
Y
hipred_score
0.608
ghis
0.509

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.757

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rtn1
Phenotype

Gene ontology

Biological process
Cellular component
endoplasmic reticulum;integral component of endoplasmic reticulum membrane
Molecular function
protein binding