RSAD2

radical S-adenosyl methionine domain containing 2, the group of Radical S-adenosylmethionine domain containing

Basic information

Region (hg38): 2:6865557-6898239

Links

ENSG00000134321NCBI:91543OMIM:607810HGNC:30908Uniprot:Q8WXG1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RSAD2 gene.

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
1
clinvar
3
clinvar
4
missense
24
clinvar
2
clinvar
1
clinvar
27
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
10
clinvar
2
clinvar
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)3494137
2-6865589-C-G not specified Uncertain significance (Sep 09, 2024)3494133
2-6865594-G-C not specified Uncertain significance (Apr 28, 2023)2520459
2-6865624-C-T not specified Likely benign (Sep 26, 2024)3494124
2-6865626-G-C not specified Uncertain significance (Sep 22, 2023)3146249
2-6865636-C-G not specified Uncertain significance (Jul 17, 2024)3494127
2-6865638-C-G not specified Uncertain significance (Aug 09, 2021)3146246
2-6865669-C-G not specified Likely benign (May 17, 2023)2528602
2-6865672-G-T CMPK2-related disorder Uncertain significance (Dec 01, 2022)2629319
2-6865684-G-A not specified Uncertain significance (Nov 13, 2024)2407401
2-6865686-G-A not specified Uncertain significance (Aug 04, 2023)2596392
2-6865687-C-A not specified Uncertain significance (Nov 25, 2024)3494139
2-6865695-A-G BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 10, AUTOSOMAL RECESSIVE Pathogenic (Nov 22, 2024)3381199
2-6865696-T-G BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 10, AUTOSOMAL RECESSIVE Pathogenic (Nov 22, 2024)3381200
2-6877812-T-C Benign (May 08, 2018)767780
2-6877864-A-C not specified Uncertain significance (May 12, 2024)3315504
2-6877890-G-A Benign (Apr 11, 2018)779067
2-6877925-T-G Benign (Apr 11, 2018)721144
2-6877983-G-T not specified Uncertain significance (Nov 24, 2024)3435698
2-6877985-A-G not specified Uncertain significance (Aug 14, 2024)3435701
2-6878014-C-A not specified Uncertain significance (Aug 19, 2024)3435699
2-6878027-A-G not specified Uncertain significance (Oct 06, 2023)3156580
2-6878042-G-A not specified Uncertain significance (Jul 12, 2023)2592367
2-6883376-G-C not specified Uncertain significance (Oct 17, 2023)3156581
2-6883444-G-A Benign (May 08, 2018)780335

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
RSAD2protein_codingprotein_codingENST00000382040 632434
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
9.44e-150.0027612555811891257480.000756
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.1741962030.9660.00001122387
Missense in Polyphen6060.0260.99957668
Synonymous0.07567474.80.9890.00000397676
Loss of Function-1.031914.71.296.21e-7197

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008400.000840
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.0001850.000185
European (Non-Finnish)0.0001590.000158
Middle Eastern0.00005440.0000544
South Asian0.004810.00468
Other0.0006590.000652

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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