RSAD2
Basic information
Region (hg38): 2:6865557-6898239
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSAD2 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 | 4 | |||||
missense | 24 | 27 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 10 | 12 | ||||
Total | 0 | 0 | 34 | 5 | 4 |
Variants in RSAD2
This is a list of pathogenic ClinVar variants found in the RSAD2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-6865588-G-A | not specified | Uncertain significance (Oct 29, 2024) | ||
2-6865589-C-G | not specified | Uncertain significance (Sep 09, 2024) | ||
2-6865594-G-C | not specified | Uncertain significance (Apr 28, 2023) | ||
2-6865624-C-T | not specified | Likely benign (Sep 26, 2024) | ||
2-6865626-G-C | not specified | Uncertain significance (Sep 22, 2023) | ||
2-6865636-C-G | not specified | Uncertain significance (Jul 17, 2024) | ||
2-6865638-C-G | not specified | Uncertain significance (Aug 09, 2021) | ||
2-6865669-C-G | not specified | Likely benign (May 17, 2023) | ||
2-6865672-G-T | CMPK2-related disorder | Uncertain significance (Dec 01, 2022) | ||
2-6865684-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
2-6865686-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
2-6865687-C-A | not specified | Uncertain significance (Nov 25, 2024) | ||
2-6865695-A-G | BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 10, AUTOSOMAL RECESSIVE | Pathogenic (Nov 22, 2024) | ||
2-6865696-T-G | BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 10, AUTOSOMAL RECESSIVE | Pathogenic (Nov 22, 2024) | ||
2-6877812-T-C | Benign (May 08, 2018) | |||
2-6877864-A-C | not specified | Uncertain significance (May 12, 2024) | ||
2-6877890-G-A | Benign (Apr 11, 2018) | |||
2-6877925-T-G | Benign (Apr 11, 2018) | |||
2-6877983-G-T | not specified | Uncertain significance (Nov 24, 2024) | ||
2-6877985-A-G | not specified | Uncertain significance (Aug 14, 2024) | ||
2-6878014-C-A | not specified | Uncertain significance (Aug 19, 2024) | ||
2-6878027-A-G | not specified | Uncertain significance (Oct 06, 2023) | ||
2-6878042-G-A | not specified | Uncertain significance (Jul 12, 2023) | ||
2-6883376-G-C | not specified | Uncertain significance (Oct 17, 2023) | ||
2-6883444-G-A | Benign (May 08, 2018) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RSAD2 | protein_coding | protein_coding | ENST00000382040 | 6 | 32434 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
9.44e-15 | 0.00276 | 125558 | 1 | 189 | 125748 | 0.000756 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.174 | 196 | 203 | 0.966 | 0.0000112 | 2387 |
Missense in Polyphen | 60 | 60.026 | 0.99957 | 668 | ||
Synonymous | 0.0756 | 74 | 74.8 | 0.989 | 0.00000397 | 676 |
Loss of Function | -1.03 | 19 | 14.7 | 1.29 | 6.21e-7 | 197 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000840 | 0.000840 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.000185 | 0.000185 |
European (Non-Finnish) | 0.000159 | 0.000158 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.00481 | 0.00468 |
Other | 0.000659 | 0.000652 |
dbNSFP
Source:
- Function
- FUNCTION: Interferon-inducible iron-sulfur (4FE-4S) cluster- binding antiviral protein which plays a major role in the cell antiviral state induced by type I and type II interferon. Can inhibit a wide range of DNA and RNA viruses, including human cytomegalovirus (HCMV), hepatitis C virus (HCV), west Nile virus (WNV), dengue virus, sindbis virus, influenza A virus, sendai virus, vesicular stomatitis virus (VSV), and human immunodeficiency virus (HIV-1). Displays antiviral activity against influenza A virus by inhibiting the budding of the virus from the plasma membrane by disturbing the lipid rafts. This is accomplished, at least in part, through binding and inhibition of the enzyme farnesyl diphosphate synthase (FPPS), which is essential for the biosynthesis of isoprenoid-derived lipids. Promotes TLR7 and TLR9-dependent production of IFN-beta production in plasmacytoid dendritic cells (pDCs) by facilitating Lys-63'- linked ubiquitination of IRAK1. Plays a role in CD4+ T-cells activation and differentiation. Facilitates T-cell receptor (TCR)- mediated GATA3 activation and optimal T-helper 2 (Th2) cytokine production by modulating NFKB1 and JUNB activities. Can inhibit secretion of soluble proteins. {ECO:0000269|PubMed:11752458, ECO:0000269|PubMed:16108059, ECO:0000269|PubMed:16982913, ECO:0000269|PubMed:17686841, ECO:0000269|PubMed:18005719, ECO:0000269|PubMed:19074433}.;
- Pathway
- Influenza A - Homo sapiens (human);Cytokine Signaling in Immune system;Immune System;Interferon alpha/beta signaling;Interferon Signaling
(Consensus)
Intolerance Scores
- loftool
- 0.477
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 50.22
Haploinsufficiency Scores
- pHI
- 0.203
- hipred
- Y
- hipred_score
- 0.593
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.138
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rsad2
- Phenotype
- homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype;
Gene ontology
- Biological process
- response to virus;viral process;positive regulation of toll-like receptor 7 signaling pathway;positive regulation of toll-like receptor 9 signaling pathway;CD4-positive, alpha-beta T cell activation;CD4-positive, alpha-beta T cell differentiation;negative regulation of viral genome replication;negative regulation of protein secretion;defense response to virus;type I interferon signaling pathway;positive regulation of T-helper 2 cell cytokine production
- Cellular component
- fibrillar center;mitochondrion;mitochondrial outer membrane;mitochondrial inner membrane;endoplasmic reticulum;endoplasmic reticulum membrane;Golgi apparatus;lipid droplet
- Molecular function
- catalytic activity;protein binding;protein self-association;metal ion binding;4 iron, 4 sulfur cluster binding