RNASE3
ribonuclease A family member 3, the group of Ribonuclease A family
Basic information
Region (hg38): 14:20891384-20892348
Previous symbols: [ "RNS3" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (14 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNASE3 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 | 0 | |||||
| missense | 10 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region ? | 0 | |||||
| non coding ? | 0 | |||||
| Total | 0 | 0 | 10 | 6 | 0 |
Variants in RNASE3
This is a list of pathogenic ClinVar variants found in the RNASE3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-20891741-A-C | not specified | Likely benign (Aug 16, 2021) | ||
| 14-20891743-G-A | not specified | Uncertain significance (Feb 14, 2023) | ||
| 14-20891745-G-C | not specified | Uncertain significance (Aug 16, 2021) | ||
| 14-20891750-G-A | not specified | Uncertain significance (Jun 21, 2022) | ||
| 14-20891784-C-T | not specified | Uncertain significance (Jan 30, 2024) | ||
| 14-20891825-C-T | not specified | Likely benign (Jan 26, 2023) | ||
| 14-20891828-C-G | not specified | Uncertain significance (May 04, 2023) | ||
| 14-20891870-T-C | not specified | Likely benign (Apr 10, 2023) | ||
| 14-20891900-C-T | Likely benign (Mar 01, 2023) | |||
| 14-20891912-G-A | not specified | Uncertain significance (Apr 22, 2022) | ||
| 14-20891913-C-T | not specified | Uncertain significance (Mar 31, 2023) | ||
| 14-20891927-G-T | not specified | Uncertain significance (May 18, 2022) | ||
| 14-20891933-G-A | Likely benign (Mar 01, 2023) | |||
| 14-20891949-G-A | not specified | Uncertain significance (Dec 07, 2021) | ||
| 14-20891985-G-A | not specified | Uncertain significance (May 24, 2023) | ||
| 14-20892047-T-C | not specified | Uncertain significance (Nov 09, 2023) | ||
| 14-20892129-G-A | not specified | Likely benign (Jul 06, 2022) | ||
| 14-20892137-G-C | not specified | Uncertain significance (Nov 17, 2023) | ||
| 14-20892146-G-C | not specified | Uncertain significance (May 05, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RNASE3 | protein_coding | protein_coding | ENST00000304639 | 1 | 950 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.423 | 107 | 95.4 | 1.12 | 0.00000579 | 1041 |
| Missense in Polyphen | 27 | 30.461 | 0.88637 | 373 | ||
| Synonymous | -0.168 | 33 | 31.8 | 1.04 | 0.00000148 | 338 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: Cytotoxin and helminthotoxin with low-efficiency ribonuclease activity. Possesses a wide variety of biological activities. Exhibits antibacterial activity, including cytoplasmic membrane depolarization of preferentially Gram-negative, but also Gram-positive strains. Promotes E.coli outer membrane detachment, alteration of the overall cell shape and partial loss of cell content. {ECO:0000269|PubMed:19450231, ECO:0000269|PubMed:2501794}.;
- Pathway
- Asthma - Homo sapiens (human);Neutrophil degranulation;Antimicrobial peptides;Innate Immune System;Immune System
(Consensus)
Recessive Scores
- pRec
- 0.170
Intolerance Scores
- loftool
- 0.673
- rvis_EVS
- 0.39
- rvis_percentile_EVS
- 76.05
Haploinsufficiency Scores
- pHI
- 0.158
- hipred
- N
- hipred_score
- 0.112
- ghis
- 0.391
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Raf1
- Phenotype
- homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; craniofacial phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); endocrine/exocrine gland phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; skeleton phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); normal phenotype; neoplasm; embryo phenotype;
Gene ontology
- Biological process
- innate immune response in mucosa;RNA catabolic process;antimicrobial humoral response;antibacterial humoral response;induction of bacterial agglutination;neutrophil degranulation;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;antimicrobial humoral immune response mediated by antimicrobial peptide;RNA phosphodiester bond hydrolysis
- Cellular component
- extracellular region;extracellular space;azurophil granule lumen
- Molecular function
- lipopolysaccharide binding;nucleic acid binding;endonuclease activity;ribonuclease activity