RSAD1

radical S-adenosyl methionine domain containing 1, the group of Radical S-adenosylmethionine domain containing

Basic information

Region (hg38): 17:50478860-50485974

Links

ENSG00000136444 ∙ NCBI:55316 ∙ ∙ HGNC:25634 ∙ Uniprot:Q9HA92 ∙ 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 RSAD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the RSAD1 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			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	1	0

Variants in RSAD1

This is a list of pathogenic ClinVar variants found in the RSAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-50478900-G-T		not specified	Uncertain significance (Dec 27, 2023)
17-50478901-C-A		not specified	Uncertain significance (Mar 19, 2024)
17-50478922-C-T		not specified	Uncertain significance (Oct 26, 2021)
17-50478952-G-A		not specified	Uncertain significance (Jun 22, 2024)
17-50478963-G-A		not specified	Uncertain significance (Apr 08, 2024)
17-50478982-C-T		not specified	Uncertain significance (Jun 05, 2024)
17-50479000-G-A		not specified	Uncertain significance (Aug 19, 2023)
17-50479009-T-C		not specified	Uncertain significance (Jan 23, 2024)
17-50479681-C-T		not specified	Uncertain significance (May 25, 2022)
17-50479986-T-G		not specified	Uncertain significance (Mar 16, 2024)
17-50480023-C-T		not specified	Uncertain significance (Apr 09, 2024)
17-50482099-T-G		not specified	Uncertain significance (Jul 19, 2023)
17-50482124-C-T		not specified	Uncertain significance (Nov 21, 2023)
17-50482128-C-T		not specified	Uncertain significance (Jan 08, 2024)
17-50482134-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-50482158-T-C		not specified	Uncertain significance (Mar 15, 2024)
17-50482167-C-T		not specified	Uncertain significance (Jun 24, 2022)
17-50482196-G-C		not specified	Uncertain significance (Dec 14, 2021)
17-50482207-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-50482218-C-T		not specified	Uncertain significance (Dec 19, 2022)
17-50482232-G-T		not specified	Uncertain significance (Jan 08, 2024)
17-50482236-C-T		not specified	Likely benign (Nov 30, 2021)
17-50482249-G-T		not specified	Uncertain significance (Oct 03, 2023)
17-50482269-A-G		not specified	Uncertain significance (May 30, 2024)
17-50482361-G-C		not specified	Uncertain significance (Feb 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
RSAD1	protein_coding	protein_coding	ENST00000258955	9	7176

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000217	0.905	125618	2	128	125748	0.000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.372	269	252	1.07	0.0000152	2763
Missense in Polyphen		97	86.713	1.1186		971
Synonymous	-0.175	110	108	1.02	0.00000606	986
Loss of Function	1.64	12	19.9	0.604	9.50e-7	215

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000653	0.000653
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000348	0.000334
Middle Eastern	0.000381	0.000381
South Asian	0.00216	0.00209
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in porphyrin cofactor biosynthesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.721
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.52

Haploinsufficiency Scores

• pHI: 0.158
• hipred: N
• hipred_score: 0.204
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Rsad1
• Phenotype: hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: porphyrin-containing compound biosynthetic process;oxidation-reduction process
• Cellular component: mitochondrion
• Molecular function: coproporphyrinogen oxidase activity;metal ion binding;4 iron, 4 sulfur cluster binding