SUMO3
Basic information
Region (hg38): 21:44805617-44818779
Previous symbols: [ "SMT3H1" ]
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 SUMO3 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 1 | 1 | 2 |
Variants in SUMO3
This is a list of pathogenic ClinVar variants found in the SUMO3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 21-44806959-T-C | not specified | Likely benign (Dec 20, 2023) | ||
| 21-44806982-G-A | Benign (Aug 02, 2017) | |||
| 21-44807021-T-C | not specified | Uncertain significance (Nov 28, 2024) | ||
| 21-44809073-T-C | not specified | Uncertain significance (Sep 22, 2023) | ||
| 21-44809109-T-C | not specified | Uncertain significance (Jul 14, 2024) | ||
| 21-44813937-G-A | Benign (May 08, 2017) | |||
| 21-44817955-T-G | not specified | Uncertain significance (Dec 03, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SUMO3 | protein_coding | protein_coding | ENST00000332859 | 4 | 13163 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.328 | 0.613 | 125735 | 0 | 1 | 125736 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.28 | 32 | 59.9 | 0.534 | 0.00000359 | 690 |
| Missense in Polyphen | 1 | 5.2279 | 0.19128 | 74 | ||
| Synonymous | 0.621 | 24 | 28.2 | 0.851 | 0.00000239 | 177 |
| Loss of Function | 1.47 | 1 | 4.29 | 0.233 | 1.83e-7 | 59 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like protein which can be covalently attached to target lysines either as a monomer or as a lysine-linked polymer. Does not seem to be involved in protein degradation and may function as an antagonist of ubiquitin in the degradation process. Plays a role in a number of cellular processes such as nuclear transport, DNA replication and repair, mitosis and signal transduction. Covalent attachment to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I, and can be promoted by an E3 ligase such as PIAS1-4, RANBP2 or CBX4 (PubMed:11451954, PubMed:18538659, PubMed:21965678). Plays a role in the regulation of sumoylation status of SETX (PubMed:24105744). {ECO:0000269|PubMed:11451954, ECO:0000269|PubMed:18538659, ECO:0000269|PubMed:21965678}.;
- Pathway
- RNA transport - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human);Exercise-induced Circadian Regulation;DNA Repair;SUMO is conjugated to E1 (UBA2:SAE1);SUMO is transferred from E1 to E2 (UBE2I, UBC9);SUMO is proteolytically processed;SUMOylation of DNA damage response and repair proteins;SUMOylation of transcription factors;SUMOylation of chromatin organization proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;basic mechanisms of sumoylation;Metabolism of proteins;Processing and activation of SUMO;SUMOylation;Formation of Incision Complex in GG-NER;Global Genome Nucleotide Excision Repair (GG-NER);Nucleotide Excision Repair
(Consensus)
Intolerance Scores
- loftool
- 0.373
- rvis_EVS
- 0.24
- rvis_percentile_EVS
- 68.72
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.628
- ghis
- 0.558
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.948
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sumo3
- Phenotype
- growth/size/body region 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); normal phenotype;
Gene ontology
- Biological process
- protein sumoylation;negative regulation of DNA binding
- Cellular component
- kinetochore;nucleus;nucleoplasm;cytoplasm;PML body
- Molecular function
- protein binding;enzyme binding;protein tag;ubiquitin-like protein ligase binding