RNASET2

ribonuclease T2

Basic information

Region (hg38): 6:166922113-166957191

Links

ENSG00000026297 ∙ NCBI:8635 ∙ OMIM:612944 ∙ HGNC:21686 ∙ Uniprot:O00584 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cystic leukoencephalopathy without megalencephaly (Definitive), mode of inheritance: AR
• cystic leukoencephalopathy without megalencephaly (Strong), mode of inheritance: AR
• cystic leukoencephalopathy without megalencephaly (Strong), mode of inheritance: AR
• cystic leukoencephalopathy without megalencephaly (Supportive), mode of inheritance: AR
• cystic leukoencephalopathy without megalencephaly (Moderate), mode of inheritance: AR
• cystic leukoencephalopathy without megalencephaly (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Leukoencephalopathy, cystic, without megalencephaly	AR	Audiologic/Otolaryngologic	Early recognition and treatment of hearing impairment may possibly benefit developmental outcomes in some individuals, including speech and language development	Audiologic/Otolaryngologic; Neurologic	9810556; 11589166; 15851732; 19525954

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RNASET2 gene.

• not provided (2 variants)
• Cystic leukoencephalopathy without megalencephaly (2 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNASET2 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				25	6	31
missense			41	6	2	49
nonsense	3					3
start loss			1			1
frameshift		1				1
inframe indel			1			1
splice donor/acceptor (+/-2bp)	1	1				2
splice region			4	7	1	12
non coding			15	16	9	40
Total	4	2	58	47	17

Highest pathogenic variant AF is 0.0000197

Variants in RNASET2

This is a list of pathogenic ClinVar variants found in the RNASET2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-166929583-GGGCATCAATGCTT-G			Uncertain significance (Dec 02, 2021)
6-166929594-C-T		RNASET2-related disorder	Likely benign (Jul 11, 2022)
6-166929608-G-A			Uncertain significance (Jun 27, 2022)
6-166929610-G-A		Inborn genetic diseases	Uncertain significance (Mar 14, 2023)
6-166929611-G-A		Cystic leukoencephalopathy without megalencephaly	Uncertain significance (Dec 03, 2018)
6-166929618-G-T		Cystic leukoencephalopathy without megalencephaly	Likely benign (Dec 11, 2023)
6-166929624-T-A			Likely benign (Jul 05, 2022)
6-166929627-G-A			Likely benign (Sep 07, 2022)
6-166929648-A-AC		Cystic leukoencephalopathy without megalencephaly • not specified	Conflicting classifications of pathogenicity (May 30, 2024)
6-166929652-C-T		Cystic leukoencephalopathy without megalencephaly • RNASET2-related disorder	Likely benign (Jan 02, 2024)
6-166929653-G-A		Cystic leukoencephalopathy without megalencephaly	Benign (Jan 30, 2024)
6-166929654-G-T		Cystic leukoencephalopathy without megalencephaly	Uncertain significance (Aug 01, 2019)
6-166929660-G-A			Likely benign (Dec 17, 2023)
6-166929662-C-T		RNASET2-related disorder	Benign (Jan 22, 2024)
6-166929663-G-A		Cystic leukoencephalopathy without megalencephaly	Benign/Likely benign (Sep 01, 2023)
6-166929679-C-G			Uncertain significance (Dec 21, 2023)
6-166929691-T-G			Uncertain significance (Feb 03, 2022)
6-166929695-G-A		Inborn genetic diseases	Uncertain significance (Mar 18, 2024)
6-166929697-G-T			Likely benign (Jan 22, 2024)
6-166929699-C-A			Likely benign (Sep 13, 2018)
6-166929699-C-T		Cystic leukoencephalopathy without megalencephaly	Conflicting classifications of pathogenicity (Feb 01, 2024)
6-166929707-C-T		Cystic leukoencephalopathy without megalencephaly	Conflicting classifications of pathogenicity (Oct 04, 2023)
6-166929711-C-G		Cystic leukoencephalopathy without megalencephaly	Conflicting classifications of pathogenicity (Jun 13, 2023)
6-166929711-C-T		Cystic leukoencephalopathy without megalencephaly	Benign (Jan 29, 2024)
6-166929712-G-A		Inborn genetic diseases	Uncertain significance (May 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RNASET2	protein_coding	protein_coding	ENST00000508775	9	27688

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000269	0.938	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.243	133	141	0.942	0.00000748	1670
Missense in Polyphen		36	45.915	0.78405		596
Synonymous	-0.445	62	57.7	1.07	0.00000361	463
Loss of Function	1.68	8	15.0	0.533	6.41e-7	168

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000139	0.000132
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has ribonuclease activity, with higher activity at acidic pH. Probably is involved in lysosomal degradation of ribosomal RNA (By similarity). Probably plays a role in cellular RNA catabolism. {ECO:0000250, ECO:0000269|PubMed:16620762, ECO:0000269|PubMed:19525954, ECO:0000269|PubMed:22735700}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.546
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.38

Haploinsufficiency Scores

• pHI: 0.0792
• hipred: N
• hipred_score: 0.132
• ghis: 0.451

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.217

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Rnaset2b
• Phenotype: renal/urinary system phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: rnaset2
• Affected structure: CNS neuron (sensu Vertebrata)
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: RNA catabolic process;neutrophil degranulation;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: extracellular region;extracellular space;lysosome;endoplasmic reticulum lumen;azurophil granule lumen;lysosomal lumen;extracellular exosome
• Molecular function: RNA binding;endoribonuclease activity;ribonuclease activity;ribonuclease T2 activity