SUMO4
Basic information
Region (hg38): 6:149400262-149401278
Previous symbols: [ "SMT3H4", "IDDM5" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (15 variants)
- not_provided (5 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUMO4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001002255.2. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 14 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 2 | 2 | ||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 14 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SUMO4 | protein_coding | protein_coding | ENST00000326669 | 1 | 683 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.164 | 48 | 51.3 | 0.935 | 0.00000260 | 624 |
| Missense in Polyphen | 4 | 4.6475 | 0.86068 | 83 | ||
| Synonymous | -0.218 | 21 | 19.8 | 1.06 | 0.00000113 | 178 |
| Loss of Function |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | ||
| East Asian | ||
| Finnish | ||
| European (Non-Finnish) | ||
| Middle Eastern | ||
| South Asian | ||
| Other |
dbNSFP
Source:
- Function
- FUNCTION: Ubiquitin-like protein which can be covalently attached to target lysines as a monomer. Does not seem to be involved in protein degradation and may modulate protein subcellular localization, stability or activity. Upon oxidative stress, conjugates to various anti-oxidant enzymes, chaperones, and stress defense proteins. May also conjugate to NFKBIA, TFAP2A and FOS, negatively regulating their transcriptional activity, and to NR3C1, positively regulating its transcriptional activity. Covalent attachment to its substrates requires prior activation by the E1 complex SAE1-SAE2 and linkage to the E2 enzyme UBE2I. {ECO:0000269|PubMed:15123604, ECO:0000269|PubMed:15247916, ECO:0000269|PubMed:16236267}.;
- Disease
- DISEASE: Diabetes mellitus, insulin-dependent, 5 (IDDM5) [MIM:600320]: A form of diabetes mellitus, a multifactorial disorder of glucose homeostasis that is characterized by susceptibility to ketoacidosis in the absence of insulin therapy. Clinical features are polydipsia, polyphagia and polyuria which result from hyperglycemia-induced osmotic diuresis and secondary thirst. These derangements result in long-term complications that affect the eyes, kidneys, nerves, and blood vessels. {ECO:0000269|PubMed:15678134, ECO:0000269|PubMed:15678135, ECO:0000269|PubMed:15678137}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.;
- Pathway
- RNA transport - Homo sapiens (human);Fluid shear stress and atherosclerosis - Homo sapiens (human)
(Consensus)
Recessive Scores
- pRec
- 0.151
Intolerance Scores
- loftool
- 0.722
- rvis_EVS
- 0.88
- rvis_percentile_EVS
- 88.96
Haploinsufficiency Scores
- pHI
- 0.216
- hipred
- N
- hipred_score
- 0.254
- ghis
- 0.405
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- protein sumoylation
- Cellular component
- nucleus
- Molecular function
- protein tag;ubiquitin-like protein ligase binding