SYVN1

synoviolin 1, the group of MicroRNA protein coding host genes|Ring finger proteins

Basic information

Region (hg38): 11:65121779-65134532

Links

ENSG00000162298 ∙ NCBI:84447 ∙ OMIM:608046 ∙ HGNC:20738 ∙ Uniprot:Q86TM6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SYVN1 gene.

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.

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	1
missense			27	2	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	27	2	2

Variants in SYVN1

This is a list of pathogenic ClinVar variants found in the SYVN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-65122417-G-A		not specified	Uncertain significance (Feb 12, 2024)
11-65124512-A-G		not specified	Uncertain significance (Feb 22, 2023)
11-65124545-CTG-C		Perrault syndrome 1	Likely pathogenic (Jan 31, 2024)
11-65125520-C-T		Perrault syndrome 1	Likely pathogenic (Jan 31, 2024)
11-65125521-G-A		Perrault syndrome 1	Likely pathogenic (Jan 31, 2024)
11-65125524-C-G		not specified	Uncertain significance (Jan 09, 2024)
11-65125526-C-T		not specified	Uncertain significance (Oct 14, 2023)
11-65125531-G-C		not specified	Uncertain significance (Apr 05, 2023)
11-65125533-A-C		Perrault syndrome 1	Likely pathogenic (Jan 31, 2024)
11-65125538-A-G		not specified	Likely benign (Jan 30, 2024)
11-65125550-A-G		not specified	Uncertain significance (Apr 08, 2022)
11-65125556-A-G		not specified	Uncertain significance (Jan 04, 2022)
11-65125560-C-T		not specified	Uncertain significance (Mar 20, 2023)
11-65125760-C-T		not specified	Uncertain significance (May 12, 2024)
11-65128390-C-T		not specified	Uncertain significance (Mar 27, 2023)
11-65128410-T-C		not specified	Uncertain significance (Jan 16, 2024)
11-65128440-T-C		not specified	Uncertain significance (Nov 08, 2022)
11-65128441-C-T		not specified	Uncertain significance (Dec 28, 2023)
11-65128451-A-T		not specified	Uncertain significance (Jun 07, 2024)
11-65128488-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-65128580-T-C		not specified	Uncertain significance (Feb 21, 2024)
11-65128593-G-A		not specified	Uncertain significance (Sep 09, 2021)
11-65128658-A-G		not specified	Likely benign (Jun 27, 2022)
11-65128664-G-C		not specified	Uncertain significance (Nov 22, 2021)
11-65128688-T-C		not specified	Likely benign (Jan 10, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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