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GeneBe

RNASEL

ribonuclease L, the group of Endoribonucleases|Ankyrin repeat domain containing

Basic information

Region (hg38): 1:182573633-182589256

Previous symbols: [ "RNS4", "PRCA1" ]

Links

ENSG00000135828NCBI:6041OMIM:180435HGNC:10050Uniprot:Q05823AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • prostate cancer, hereditary, 1 (Limited), mode of inheritance: AD
  • prostate cancer, hereditary, 1 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Prostate cancer, hereditary, 1ADOncologicSurveillance and early diagnosis could potentially be beneficialOncologic11799394; 12022038; 12915880; 16054567; 17224235; 18575592
Variants may be involved in susceptibility to multiple cancer types

ClinVar

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

  • Inborn genetic diseases (14 variants)
  • not provided (7 variants)
  • Prostate cancer, hereditary, 1 (6 variants)
  • Ovarian cancer (5 variants)
  • Malignant tumor of prostate (1 variants)
  • not specified (1 variants)
  • Hereditary cancer (1 variants)
  • Prostate cancer, susceptibility to (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNASEL 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
4
clinvar
4
missense
2
clinvar
16
clinvar
3
clinvar
4
clinvar
25
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
0
non coding
0
Total 0 2 18 4 8

Highest pathogenic variant AF is 0.0000525

Variants in RNASEL

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

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

Position Type Phenotype Significance ClinVar
1-182575424-C-T Inborn genetic diseases Uncertain significance (Mar 02, 2023)2459893
1-182575430-C-T Inborn genetic diseases Uncertain significance (Mar 20, 2023)2527371
1-182575446-C-T RNASEL-related condition Benign (Jan 27, 2020)3055991
1-182575466-G-T Ovarian cancer Benign (Jan 01, 2022)2445292
1-182576254-AC-A Prostate cancer, hereditary, 1 Uncertain significance (-)3024086
1-182581307-C-T Inborn genetic diseases Uncertain significance (Mar 23, 2022)2220846
1-182581320-C-T Inborn genetic diseases Uncertain significance (May 30, 2023)2523909
1-182582129-G-A Inborn genetic diseases Uncertain significance (Aug 21, 2023)2620301
1-182582234-C-T Prostate cancer, hereditary, 1 Uncertain significance (Jul 07, 2023)2573176
1-182584167-C-A Prostate cancer, hereditary, 1 Uncertain significance (Mar 10, 2022)2435442
1-182585330-T-C Inborn genetic diseases Uncertain significance (Dec 13, 2022)2334328
1-182585338-T-C Ovarian cancer Likely pathogenic (Jan 01, 2022)2445376
1-182585376-CA-C Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702921
1-182585378-A-T Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702877
1-182585385-T-A Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702875
1-182585389-T-G Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702874
1-182585391-A-G Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702929
1-182585391-AAC-A Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702919
1-182585393-CA-C Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702918
1-182585395-G-A Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702873
1-182585395-GC-G Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702917
1-182585398-T-G Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702872
1-182585399-TA-T Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702916
1-182585400-A-T Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702871
1-182585402-A-T Prostate cancer, hereditary, 1 Uncertain significance (Aug 17, 2022)1702870

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RNASELprotein_codingprotein_codingENST00000367559 615623
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.95e-100.405124628311141257450.00445
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1593863950.9770.00002164915
Missense in Polyphen128127.921.00061606
Synonymous0.5501481570.9440.000008901433
Loss of Function1.061823.60.7640.00000137296

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.002680.00267
Ashkenazi Jewish0.01540.0151
East Asian0.0007080.000707
Finnish0.008270.00830
European (Non-Finnish)0.005470.00539
Middle Eastern0.0007080.000707
South Asian0.001930.00193
Other0.003940.00392

dbNSFP

Source: dbNSFP

Function
FUNCTION: Endoribonuclease that functions in the interferon (IFN) antiviral response. In INF treated and virus infected cells, RNASEL probably mediates its antiviral effects through a combination of direct cleavage of single-stranded viral RNAs, inhibition of protein synthesis through the degradation of rRNA, induction of apoptosis, and induction of other antiviral genes. RNASEL mediated apoptosis is the result of a JNK-dependent stress- response pathway leading to cytochrome c release from mitochondria and caspase-dependent apoptosis. Therefore, activation of RNASEL could lead to elimination of virus infected cells under some circumstances. In the crosstalk between autophagy and apoptosis proposed to induce autophagy as an early stress response to small double-stranded RNA and at later stages of prolonged stress to activate caspase-dependent proteolytic cleavage of BECN1 to terminate autophagy and promote apoptosis (PubMed:26263979). Might play a central role in the regulation of mRNA turnover (PubMed:11585831). Cleaves 3' of UpNp dimers, with preference for UU and UA sequences, to sets of discrete products ranging from between 4 and 22 nucleotides in length. {ECO:0000269|PubMed:11585831, ECO:0000269|PubMed:26263979}.;
Disease
DISEASE: Prostate cancer, hereditary, 1 (HPC1) [MIM:601518]: A condition associated with familial predisposition to cancer of the prostate. Most prostate cancers are adenocarcinomas that develop in the acini of the prostatic ducts. Other rare histopathologic types of prostate cancer that occur in approximately 5% of patients include small cell carcinoma, mucinous carcinoma, prostatic ductal carcinoma, transitional cell carcinoma, squamous cell carcinoma, basal cell carcinoma, adenoid cystic carcinoma (basaloid), signet-ring cell carcinoma and neuroendocrine carcinoma. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry. {ECO:0000305|PubMed:11799394, ECO:0000305|PubMed:11941539, ECO:0000305|PubMed:12415269, ECO:0000305|PubMed:17344846}.;
Pathway
Influenza A - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Senescence and Autophagy in Cancer;Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

pRec
0.121

Intolerance Scores

loftool
0.685
rvis_EVS
-0.17
rvis_percentile_EVS
40.63

Haploinsufficiency Scores

pHI
0.0611
hipred
N
hipred_score
0.211
ghis
0.491

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.255

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Rnasel
Phenotype
cellular phenotype; endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process
rRNA processing;mRNA processing;protein phosphorylation;regulation of mRNA stability;negative regulation of viral genome replication;fat cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of glucose import;defense response to virus;type I interferon signaling pathway;regulation of type I interferon-mediated signaling pathway;RNA phosphodiester bond hydrolysis, endonucleolytic
Cellular component
cellular_component;mitochondrial matrix;cytosol;nuclear matrix
Molecular function
RNA binding;endoribonuclease activity;protein kinase activity;protein binding;ATP binding;rRNA binding;ribonucleoprotein complex binding;metal ion binding