SYVN1
synoviolin 1, the group of MicroRNA protein coding host genes|Ring finger proteins
Basic information
Region (hg38): 11:65121780-65134532
Links
Phenotypes
GenCC
Source:
- schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (67 variants)
- not_provided (2 variants)
- Encephalomalacia (2 variants)
- Intellectual_disability,_moderate (2 variants)
- Hypotonia (2 variants)
- Tracheomalacia (2 variants)
- Periventricular_leukomalacia (2 variants)
- Hypospadias (2 variants)
- Abnormal_facial_shape (2 variants)
- Seizure (2 variants)
- Delayed_speech_and_language_development (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SYVN1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000172230.3. 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 | 65 | 68 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 65 | 2 | 2 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYVN1 | protein_coding | protein_coding | ENST00000377190 | 15 | 12753 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000298 | 125743 | 0 | 5 | 125748 | 0.0000199 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.18 | 248 | 365 | 0.679 | 0.0000214 | 3958 |
| Missense in Polyphen | 27 | 87.827 | 0.30742 | 1013 | ||
| Synonymous | -0.105 | 139 | 137 | 1.01 | 0.00000752 | 1320 |
| Loss of Function | 4.70 | 1 | 27.7 | 0.0362 | 0.00000146 | 299 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000290 | 0.0000290 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000176 | 0.0000176 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000344 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Acts as an E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Component of the endoplasmic reticulum quality control (ERQC) system also called ER-associated degradation (ERAD) involved in ubiquitin-dependent degradation of misfolded endoplasmic reticulum proteins (PubMed:12459480, PubMed:12646171, PubMed:12975321, PubMed:14593114, PubMed:16289116, PubMed:16847254, PubMed:17059562, PubMed:17141218, PubMed:17170702, PubMed:22607976, PubMed:26471130). Also promotes the degradation of normal but naturally short-lived proteins such as SGK. Protects cells from ER stress-induced apoptosis. Protects neurons from apoptosis induced by polyglutamine-expanded huntingtin (HTT) or unfolded GPR37 by promoting their degradation (PubMed:17141218). Sequesters p53/TP53 in the cytoplasm and promotes its degradation, thereby negatively regulating its biological function in transcription, cell cycle regulation and apoptosis (PubMed:17170702). Mediates the ubiquitination and subsequent degradation of cytoplasmic NFE2L1 (By similarity). {ECO:0000250|UniProtKB:Q9DBY1, ECO:0000269|PubMed:12459480, ECO:0000269|PubMed:12646171, ECO:0000269|PubMed:12975321, ECO:0000269|PubMed:14593114, ECO:0000269|PubMed:16289116, ECO:0000269|PubMed:16847254, ECO:0000269|PubMed:17059562, ECO:0000269|PubMed:17141218, ECO:0000269|PubMed:17170702, ECO:0000269|PubMed:22607976, ECO:0000269|PubMed:26471130}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);XBP1(S) activates chaperone genes;Disease;Signal Transduction;ER Quality Control Compartment (ERQC);Calnexin/calreticulin cycle;Post-translational protein modification;Metabolism of proteins;Hedgehog ligand biogenesis;Signaling by Hedgehog;Asparagine N-linked glycosylation;N-glycan trimming in the ER and Calnexin/Calreticulin cycle;Hh mutants that don,t undergo autocatalytic processing are degraded by ERAD;Hh mutants abrogate ligand secretion;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- loftool
- 0.169
- rvis_EVS
- -0.73
- rvis_percentile_EVS
- 14.02
Haploinsufficiency Scores
- pHI
- 0.590
- hipred
- Y
- hipred_score
- 0.771
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.566
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syvn1
- Phenotype
- cellular phenotype; immune system 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); skeleton phenotype;
Gene ontology
- Biological process
- ubiquitin-dependent protein catabolic process;protein ubiquitination;protein N-linked glycosylation via asparagine;ubiquitin-dependent ERAD pathway;endoplasmic reticulum unfolded protein response;retrograde protein transport, ER to cytosol;IRE1-mediated unfolded protein response;ERAD pathway;protein stabilization;protein K48-linked ubiquitination;negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway;endoplasmic reticulum mannose trimming
- Cellular component
- Hrd1p ubiquitin ligase complex;Hrd1p ubiquitin ligase ERAD-L complex;nucleoplasm;endoplasmic reticulum;endoplasmic reticulum membrane;smooth endoplasmic reticulum;membrane;integral component of endoplasmic reticulum membrane;Derlin-1 retrotranslocation complex;endoplasmic reticulum quality control compartment
- Molecular function
- protein binding;metal ion binding;unfolded protein binding;chaperone binding;ATPase binding;ubiquitin protein ligase activity;ubiquitin-specific protease binding