OAS1
Basic information
Region (hg38): 12:112905856-112933219
Previous symbols: [ "OIAS" ]
Links
Phenotypes
GenCC
Source:
- pulmonary alveolar proteinosis with hypogammaglobulinemia (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Immunodeficiency 100 with pulmonary alveolar proteinosis and hypogammaglobulinemia | AD | Allergy/Immunology/Infectious; Pulmonary | Recurrent infections have been described, and preventive measures and awareness allowing early diagnosis and aggressive treatmentment of infections may be beneficial; Individuals may suffer from severe and early-onset respiratory insufficiency, and early awareness may be beneficial for pulmonary management, including related to ventilatory support; HSCT has been described | Allergy/Immunology/Infectious; Pulmonary | 29185156; 29455859; 34145065 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (298 variants)
- not_specified (54 variants)
- Pulmonary_alveolar_proteinosis_with_hypogammaglobulinemia (11 variants)
- OAS1-related_disorder (11 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the OAS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016816.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 61 | 68 | ||||
missense | 128 | 45 | 15 | 191 | ||
nonsense | 7 | |||||
start loss | 2 | 2 | ||||
frameshift | 9 | |||||
splice donor/acceptor (+/-2bp) | 5 | |||||
Total | 1 | 2 | 148 | 110 | 21 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
OAS1 | protein_coding | protein_coding | ENST00000445409 | 6 | 25409 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000345 | 0.950 | 125659 | 0 | 89 | 125748 | 0.000354 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -0.426 | 247 | 229 | 1.08 | 0.0000124 | 2697 |
Missense in Polyphen | 89 | 83.797 | 1.0621 | 1020 | ||
Synonymous | 1.14 | 80 | 94.0 | 0.851 | 0.00000524 | 809 |
Loss of Function | 1.80 | 10 | 18.3 | 0.546 | 0.00000100 | 197 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00104 | 0.00104 |
Ashkenazi Jewish | 0.0000993 | 0.0000992 |
East Asian | 0.00207 | 0.00207 |
Finnish | 0.000370 | 0.000370 |
European (Non-Finnish) | 0.000123 | 0.000123 |
Middle Eastern | 0.00207 | 0.00207 |
South Asian | 0.0000980 | 0.0000980 |
Other | 0.000815 | 0.000815 |
dbNSFP
Source:
- 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 higher oligomers 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. The secreted form displays antiviral effect against vesicular stomatitis virus (VSV), herpes simplex virus type 2 (HSV-2), and encephalomyocarditis virus (EMCV) and stimulates the alternative antiviral pathway independent of RNase L. {ECO:0000269|PubMed:12799444, ECO:0000269|PubMed:18931074, ECO:0000269|PubMed:19923450, ECO:0000269|PubMed:23319625}.;
- 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);The human immune response to tuberculosis;Type II interferon signaling (IFNG);Cytokine Signaling in Immune system;Immune System;Interferon gamma signaling;Interferon alpha/beta signaling;Interferon Signaling
(Consensus)
Recessive Scores
- pRec
- 0.190
Intolerance Scores
- loftool
- 0.979
- rvis_EVS
- 1.31
- rvis_percentile_EVS
- 94.04
Haploinsufficiency Scores
- pHI
- 0.0239
- hipred
- N
- hipred_score
- 0.145
- ghis
- 0.479
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.613
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Oas1h
- Phenotype
Gene ontology
- Biological process
- glucose metabolic process;response to virus;glucose homeostasis;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 region;nucleus;nucleoplasm;cytoplasm;mitochondrion;endoplasmic reticulum;cytosol
- Molecular function
- 2'-5'-oligoadenylate synthetase activity;double-stranded RNA binding;protein binding;ATP binding;metal ion binding