OAS2

2'-5'-oligoadenylate synthetase 2, the group of 2'-5'-oligoadenylate synthetase family

Basic information

Region (hg38): 12:112978395-113011723

Links

ENSG00000111335 ∙ NCBI:4939 ∙ OMIM:603350 ∙ HGNC:8087 ∙ Uniprot:P29728 ∙ 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 OAS2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OAS2 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				1	3	4
missense			39	5		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	39	6	3

Variants in OAS2

This is a list of pathogenic ClinVar variants found in the OAS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-112978645-G-A		not specified	Uncertain significance (Oct 06, 2022)
12-112978720-G-A		not specified	Uncertain significance (Dec 16, 2022)
12-112978750-C-T		not specified	Uncertain significance (Jul 19, 2023)
12-112978758-G-A			Benign (Mar 29, 2018)
12-112978775-G-A		not specified	Uncertain significance (Aug 12, 2021)
12-112987047-T-G		not specified	Uncertain significance (Nov 22, 2021)
12-112987054-G-A		not specified	Uncertain significance (Apr 22, 2024)
12-112987128-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-112987151-C-G		not specified	Uncertain significance (Sep 13, 2023)
12-112987209-A-G		not specified	Uncertain significance (Feb 21, 2024)
12-112987214-C-G		not specified	Uncertain significance (May 31, 2023)
12-112987289-G-A			Likely benign (Dec 31, 2019)
12-112995310-C-A		not specified	Uncertain significance (Dec 07, 2021)
12-112995314-G-T		not specified	Uncertain significance (Feb 07, 2023)
12-112995319-T-C		not specified	Uncertain significance (Jun 03, 2022)
12-112997557-C-T		not specified	Uncertain significance (Jul 06, 2021)
12-112997602-G-A		not specified	Uncertain significance (May 10, 2024)
12-112997634-G-A		not specified	Likely benign (May 20, 2024)
12-112997643-G-A		not specified	Likely benign (Jun 06, 2023)
12-112997662-G-T		not specified	Uncertain significance (Jul 12, 2022)
12-112997689-T-C		not specified	Likely benign (May 02, 2024)
12-112997701-A-T		not specified	Uncertain significance (Jan 26, 2023)
12-112998295-C-T		not specified	Uncertain significance (Jun 07, 2024)
12-113002948-C-T		not specified	Uncertain significance (Oct 31, 2022)
12-113002966-T-C		not specified	Uncertain significance (Mar 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OAS2	protein_coding	protein_coding	ENST00000342315	11	33329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.61e-21	0.00365	125588	0	159	125747	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.378	371	392	0.946	0.0000215	4728
Missense in Polyphen		118	129.28	0.91275		1719
Synonymous	-0.0868	161	160	1.01	0.00000930	1347
Loss of Function	0.365	33	35.3	0.934	0.00000174	399

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00404	0.00404
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000492	0.000489
Finnish	0.000278	0.000277
European (Non-Finnish)	0.000346	0.000334
Middle Eastern	0.000492	0.000489
South Asian	0.000622	0.000621
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response (PubMed:10464285, PubMed:9880569). Activated by detection of double stranded RNA (dsRNA): polymerizes higher oligomers of 2'- 5'-oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNASEL) leading to its dimerization and subsequent activation (PubMed:10464285, PubMed:9880569, PubMed:11682059). Activation of RNASEL leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication (PubMed:10464285, PubMed:9880569). Can mediate the antiviral effect via the classical RNASEL-dependent pathway or an alternative antiviral pathway independent of RNASEL (PubMed:21142819). In addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation (PubMed:21142819). May act as a negative regulator of lactation, stopping lactation in virally infected mammary gland lobules, thereby preventing transmission of viruses to neonates (By similarity). Non-infected lobules would not be affected, allowing efficient pup feeding during infection (By similarity). {ECO:0000250|UniProtKB:E9Q9A9, ECO:0000269|PubMed:10464285, ECO:0000269|PubMed:11682059, ECO:0000269|PubMed:19923450, ECO:0000269|PubMed:9880569, ECO:0000303|PubMed:21142819}.
• Pathway: Influenza A - Homo sapiens (human);NOD-like receptor signaling pathway - Homo sapiens (human);Hepatitis C - Homo sapiens (human);Measles - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon alpha/beta signaling;Interferon Signaling (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.983
• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.2

Haploinsufficiency Scores

• pHI: 0.0791
• hipred: N
• hipred_score: 0.153
• ghis: 0.590

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.186

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oas2
• Phenotype: endocrine/exocrine gland 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); cellular phenotype

Gene ontology

• Biological process: nucleobase-containing compound metabolic process;RNA catabolic process;response to virus;response to bacterium;defense response to virus;interferon-gamma-mediated signaling pathway;type I interferon signaling pathway;regulation of ribonuclease activity;regulation of lactation
• Cellular component: nucleus;nucleoplasm;cytosol;membrane;intracellular membrane-bounded organelle;perinuclear region of cytoplasm
• Molecular function: 2'-5'-oligoadenylate synthetase activity;double-stranded RNA binding;protein binding;ATP binding;metal ion binding