RNASE3

ribonuclease A family member 3, the group of Ribonuclease A family

Basic information

Region (hg38): 14:20891385-20892348

Previous symbols: [ "RNS3" ]

Links

ENSG00000169397 ∙ NCBI:6037 ∙ OMIM:131398 ∙ HGNC:10046 ∙ Uniprot:P12724 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNASE3 gene.

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			17	7		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	7	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)
14-20891789-G-A		not specified	Uncertain significance (Feb 20, 2025)
14-20891825-C-T		not specified	Likely benign (Jan 26, 2023)
14-20891828-C-G		not specified	Uncertain significance (May 04, 2023)
14-20891849-C-T		not specified	Uncertain significance (Sep 01, 2024)
14-20891870-T-C		not specified	Likely benign (Apr 10, 2023)
14-20891900-C-T			Likely benign (Mar 01, 2023)
14-20891901-G-A		not specified	Likely benign (Nov 13, 2024)
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 (Aug 19, 2024)
14-20891933-G-A			Likely benign (Mar 01, 2023)
14-20891949-G-A		not specified	Uncertain significance (Dec 07, 2021)
14-20891970-T-A		not specified	Uncertain significance (Sep 02, 2024)
14-20891985-G-A		not specified	Uncertain significance (May 24, 2023)
14-20891996-C-T		not specified	Uncertain significance (Sep 24, 2024)
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)
14-20892146-G-T		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

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: dbNSFP

• 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