OAS3

2'-5'-oligoadenylate synthetase 3, the group of 2'-5'-oligoadenylate synthetase family

Basic information

Region (hg38): 12:112938050-112976460

Links

ENSG00000111331 ∙ NCBI:4940 ∙ OMIM:603351 ∙ HGNC:8088 ∙ Uniprot:Q9Y6K5 ∙ 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 OAS3 gene.

• Inborn genetic diseases (49 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OAS3 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			47	2	4	53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	2	4

Variants in OAS3

This is a list of pathogenic ClinVar variants found in the OAS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-112938609-G-A		not specified	Uncertain significance (Jun 21, 2021)
12-112938622-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-112938651-A-T		not specified	Uncertain significance (Jul 08, 2022)
12-112938654-G-A		not specified	Uncertain significance (Dec 11, 2023)
12-112938658-G-C		not specified	Uncertain significance (Aug 11, 2022)
12-112938675-G-A			Benign (Jun 18, 2018)
12-112938687-C-T		not specified	Uncertain significance (Mar 29, 2023)
12-112938688-G-A		not specified	Uncertain significance (Sep 21, 2023)
12-112941570-G-A		not specified	Uncertain significance (Feb 28, 2023)
12-112941673-G-A		not specified	Uncertain significance (Feb 07, 2023)
12-112941756-G-A		not specified	Uncertain significance (Dec 19, 2022)
12-112941785-C-G		not specified	Uncertain significance (Jan 22, 2024)
12-112944521-C-T		not specified	Uncertain significance (Mar 06, 2023)
12-112944550-G-A		not specified	Uncertain significance (Jul 14, 2021)
12-112944598-C-T		not specified	Uncertain significance (Nov 08, 2022)
12-112944644-A-G		not specified	Uncertain significance (May 16, 2023)
12-112946795-A-G		not specified	Uncertain significance (Jan 19, 2022)
12-112946824-G-A		not specified	Uncertain significance (Mar 24, 2023)
12-112946932-G-A		not specified	Uncertain significance (Jul 13, 2022)
12-112946950-C-A		not specified	Uncertain significance (Sep 07, 2022)
12-112946951-A-G		not specified	Uncertain significance (Dec 15, 2021)
12-112947957-T-C		not specified	Uncertain significance (Dec 16, 2023)
12-112947977-T-G		not specified	Uncertain significance (Sep 26, 2023)
12-112948031-G-A		not specified	Uncertain significance (Dec 11, 2023)
12-112948885-G-A		not specified	Uncertain significance (Feb 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OAS3	protein_coding	protein_coding	ENST00000228928	16	34898

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.97e-33	0.0000182	121765	21	2909	124695	0.0118

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.255	597	615	0.971	0.0000369	7011
Missense in Polyphen		179	178.93	1.0004		2142
Synonymous	-0.00639	265	265	1.00	0.0000159	2209
Loss of Function	-0.0212	50	49.8	1.00	0.00000247	532

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00825	0.00822
Ashkenazi Jewish	0.0172	0.0172
East Asian	0.00531	0.00507
Finnish	0.0166	0.0165
European (Non-Finnish)	0.0166	0.0164
Middle Eastern	0.00531	0.00507
South Asian	0.00583	0.00580
Other	0.0130	0.0128

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Interferon-induced, dsRNA-activated antiviral enzyme which plays a critical role in cellular innate antiviral response. In addition, it may also play a role in other cellular processes such as apoptosis, cell growth, differentiation and gene regulation. Synthesizes preferentially dimers of 2'-5'- oligoadenylates (2-5A) from ATP which then bind to the inactive monomeric form of ribonuclease L (RNase L) leading to its dimerization and subsequent activation. Activation of RNase L leads to degradation of cellular as well as viral RNA, resulting in the inhibition of protein synthesis, thus terminating viral replication. Can mediate the antiviral effect via the classical RNase L-dependent pathway or an alternative antiviral pathway independent of RNase L. Displays antiviral activity against Chikungunya virus (CHIKV), Dengue virus, Sindbis virus (SINV) and Semliki forest virus (SFV). {ECO:0000269|PubMed:19056102, ECO:0000269|PubMed:19923450, ECO:0000269|PubMed:9880533}.
• 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)

Intolerance Scores

• loftool: 0.974
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.98

Haploinsufficiency Scores

• pHI: 0.0941
• hipred: N
• hipred_score: 0.146
• ghis: 0.561

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oas3

Gene ontology

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