RSAD2

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

Basic information

Region (hg38): 2:6865557-6898239

Links

ENSG00000134321 ∙ NCBI:91543 ∙ OMIM:607810 ∙ HGNC:30908 ∙ Uniprot:Q8WXG1 ∙ 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 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	3	4
missense			24	2	1	27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			10	2		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: gnomAD

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: 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

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