SOD3

superoxide dismutase 3, the group of Superoxide dismutases

Basic information

Region (hg38): 4:24789911-24800842

Links

ENSG00000109610 ∙ NCBI:6649 ∙ OMIM:185490 ∙ HGNC:11181 ∙ Uniprot:P08294 ∙ 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 SOD3 gene.

• Inborn genetic diseases (20 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOD3 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	2	3
missense			20		1	21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	3

Variants in SOD3

This is a list of pathogenic ClinVar variants found in the SOD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-24799530-G-C			Benign (May 24, 2018)
4-24799553-T-A		not specified	Uncertain significance (Aug 02, 2023)
4-24799572-C-A		not specified	Uncertain significance (Aug 15, 2023)
4-24799580-C-T		not specified	Uncertain significance (Jun 02, 2023)
4-24799604-A-G		SOD3-related disorder	Likely benign (May 31, 2022)
4-24799614-G-A			Benign (Mar 29, 2018)
4-24799638-C-T		SOD3-related disorder	Likely benign (Sep 24, 2019)
4-24799664-A-T		not specified	Uncertain significance (May 28, 2023)
4-24799665-G-C		not specified	Uncertain significance (May 28, 2023)
4-24799679-G-C		not specified	Uncertain significance (Feb 15, 2023)
4-24799687-G-A		not specified	Uncertain significance (Sep 01, 2021)
4-24799690-G-C		not specified	Uncertain significance (Sep 06, 2022)
4-24799693-G-A		SOD3-related disorder	Benign (Oct 17, 2019)
4-24799732-C-T		SOD3-related disorder	Benign (Oct 21, 2019)
4-24799786-C-A		not specified	Uncertain significance (Feb 06, 2023)
4-24799792-G-A		SOD3-related disorder	Benign (Oct 01, 2019)
4-24799834-G-C		not specified	Likely benign (Feb 26, 2024)
4-24799877-G-C		not specified	Uncertain significance (Jun 16, 2023)
4-24799887-C-A		not specified	Uncertain significance (Sep 17, 2021)
4-24799922-C-T		not specified	Uncertain significance (Sep 14, 2023)
4-24799970-C-T		not specified	Uncertain significance (Jan 09, 2024)
4-24799997-A-G		not specified	Uncertain significance (Nov 04, 2022)
4-24800003-C-T		not specified	Uncertain significance (Sep 14, 2022)
4-24800023-G-A		not specified	Uncertain significance (Feb 23, 2023)
4-24800030-C-A		not specified	Uncertain significance (May 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOD3	protein_coding	protein_coding	ENST00000382120	1	10931

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000723	0.538	119594	0	62	119656	0.000259

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.11	101	138	0.734	0.00000928	1467
Missense in Polyphen		29	45.346	0.63953		561
Synonymous	1.24	60	73.6	0.815	0.00000560	517
Loss of Function	0.350	5	5.92	0.845	3.43e-7	46

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00136	0.00136
Ashkenazi Jewish	0.00	0.00
East Asian	0.000119	0.000112
Finnish	0.00	0.00
European (Non-Finnish)	0.0000697	0.0000648
Middle Eastern	0.000119	0.000112
South Asian	0.000103	0.0000992
Other	0.000894	0.000845

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Protect the extracellular space from toxic effect of reactive oxygen intermediates by converting superoxide radicals into hydrogen peroxide and oxygen.
• Pathway: Degradation of Superoxides;Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Nuclear Receptors Meta-Pathway;NRF2 pathway;Copper homeostasis;One carbon metabolism and related pathways;Oxidative Stress;Detoxification of Reactive Oxygen Species;cardiac protection against ros;Cellular responses to stress;Cellular responses to external stimuli;the igf-1 receptor and longevity;reactive oxygen species degradation (Consensus)

Recessive Scores

• pRec: 0.106

Haploinsufficiency Scores

• pHI: 0.213
• hipred: N
• hipred_score: 0.461
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sod3
• Phenotype: normal 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; skeleton phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: response to hypoxia;removal of superoxide radicals;cellular response to oxidative stress;positive regulation of catalytic activity;response to copper ion;oxidation-reduction process
• Cellular component: extracellular region;extracellular space;nucleus;cytoplasm;Golgi lumen;collagen-containing extracellular matrix;extracellular exosome
• Molecular function: superoxide dismutase activity;copper ion binding;protein binding;heparin binding;zinc ion binding;superoxide dismutase copper chaperone activity