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SYVN1 synoviolin 1 [ Homo sapiens (human) ]

Gene ID: 84447, updated on 11-Apr-2024

Summary

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Official Symbol
SYVN1provided by HGNC
Official Full Name
synoviolin 1provided by HGNC
Primary source
HGNC:HGNC:20738
See related
Ensembl:ENSG00000162298 MIM:608046; AllianceGenome:HGNC:20738
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DER3; HRD1
Summary
This gene encodes a protein involved in endoplasmic reticulum (ER)-associated degradation. The encoded protein removes unfolded proteins, accumulated during ER stress, by retrograde transport to the cytosol from the ER. This protein also uses the ubiquitin-proteasome system for additional degradation of unfolded proteins. Sequence analysis identified two transcript variants that encode different isoforms. [provided by RefSeq, May 2011]
Expression
Ubiquitous expression in lymph node (RPKM 27.2), appendix (RPKM 21.7) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q13.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (65127279..65134519, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (65120558..65127829, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (64894751..64901990, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64883502-64884046 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64884593-64885136 Neighboring gene Sharpr-MPRA regulatory region 3974 Neighboring gene zinc finger HIT-type containing 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4944 Neighboring gene FAU ubiquitin like and ribosomal protein S30 fusion Neighboring gene mitochondrial ribosomal protein L49 Neighboring gene microRNA 6751 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4945 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:64900593-64900769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4946 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:64901729-64902632 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 10 Neighboring gene RNA, U2 small nuclear 23, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Unique RING finger structure from the human HRD1 protein. Miyamoto K, et al. Protein Sci, 2019 Feb. PMID 30345569, Free PMC Article
  2. Upregulation of HRD1 promotes cell migration and invasion in colon cancer. Tan X, et al. Mol Cell Biochem, 2019 Apr. PMID 30306455
  3. Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1. Hwang J, et al. J Biol Chem, 2017 Jun 2. PMID 28411238, Free PMC Article
  4. A critical role of Hrd1 in the regulation of optineurin degradation and aggresome formation. Mao J, et al. Hum Mol Genet, 2017 May 15. PMID 28334804
  5. MHC class I molecules are preferentially ubiquitinated on endoplasmic reticulum luminal residues during HRD1 ubiquitin E3 ligase-mediated dislocation. Burr ML, et al. Proc Natl Acad Sci U S A, 2013 Aug 27. PMID 23929775, Free PMC Article

See all (181) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. HRD1-induced TMEM2 ubiquitination promotes ER stress-mediated apoptosis through a non-canonical pathway in intestinal ischemia/reperfusion.
    Title: HRD1-induced TMEM2 ubiquitination promotes ER stress-mediated apoptosis through a non-canonical pathway in intestinal ischemia/reperfusion.
  2. Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.
    Title: Hypomorphic human SEL1L and HRD1 variants uncouple multilayered ER-associated degradation machinery.
  3. Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders.
    Title: Hypomorphic variants of SEL1L-HRD1 ER-associated degradation are associated with neurodevelopmental disorders.
  4. Exogenous H2 S promotes ubiquitin-mediated degradation of SREBP1 to alleviate diabetic cardiomyopathy via SYVN1 S-sulfhydration.
    Title: Exogenous H(2) S promotes ubiquitin-mediated degradation of SREBP1 to alleviate diabetic cardiomyopathy via SYVN1 S-sulfhydration.
  5. SYVN1-mediated ubiquitylation directs localization of MCT4 in the plasma membrane to promote the progression of lung adenocarcinoma.
    Title: SYVN1-mediated ubiquitylation directs localization of MCT4 in the plasma membrane to promote the progression of lung adenocarcinoma.
  6. SLC35F2-SYVN1-TRIM59 axis critically regulates ferroptosis of pancreatic cancer cells by inhibiting endogenous p53.
    Title: SLC35F2-SYVN1-TRIM59 axis critically regulates ferroptosis of pancreatic cancer cells by inhibiting endogenous p53.
  7. Association between SYVN1 and SEL1 genetic polymorphisms and remission in rheumatoid arthritis patients treated with TNF-alpha inhibitors: a machine learning approach.
    Title: Association between SYVN1 and SEL1 genetic polymorphisms and remission in rheumatoid arthritis patients treated with TNF-α inhibitors: a machine learning approach.
  8. SYVN1 Promotes STAT3 Protein Ubiquitination and Exerts Antiangiogenesis Effects in Retinopathy of Prematurity Development.
    Title: SYVN1 Promotes STAT3 Protein Ubiquitination and Exerts Antiangiogenesis Effects in Retinopathy of Prematurity Development.
  9. Endoplasmic reticulum stress-triggered ferroptosis via the XBP1-Hrd1-Nrf2 pathway induces EMT progression in diabetic nephropathy.
    Title: Endoplasmic reticulum stress-triggered ferroptosis via the XBP1-Hrd1-Nrf2 pathway induces EMT progression in diabetic nephropathy.
  10. miR-602 Activates NRF2 Antioxidant Pathways to Protect HBMECs from OGD/R-Induced Oxidative Stress via Targeting KEAP1 and HRD1.
    Title: miR-602 Activates NRF2 Antioxidant Pathways to Protect HBMECs from OGD/R-Induced Oxidative Stress via Targeting KEAP1 and HRD1.
Submit: New GeneRIF Correction See all GeneRIFs (85)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA1810, MGC40372

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATPase binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein-folding chaperone binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables ubiquitin protein ligase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ubiquitin protein ligase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables ubiquitin protein ligase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables ubiquitin protein ligase activity TAS
Traceable Author Statement
more info
 PubMed 
enables ubiquitin-specific protease binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables unfolded protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in ERAD pathway IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ERAD pathway IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ERAD pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ERAD pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in immature B cell differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway TAS
Traceable Author Statement
more info
 PubMed 
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K48-linked ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein ubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination TAS
Traceable Author Statement
more info
 PubMed 
involved_in retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in ubiquitin-dependent protein catabolic process TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of Derlin-1 retrotranslocation complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Hrd1p ubiquitin ligase ERAD-L complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of Hrd1p ubiquitin ligase ERAD-L complex IMP
Inferred from Mutant Phenotype
more info
 PubMed 
part_of Hrd1p ubiquitin ligase complex TAS
Traceable Author Statement
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in endomembrane system IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum TAS
Traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
is_active_in endoplasmic reticulum quality control compartment IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in endoplasmic reticulum quality control compartment IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum quality control compartment TAS
Traceable Author Statement
more info
 PubMed 
located_in membrane HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in smooth endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
E3 ubiquitin-protein ligase synoviolin
Names
HMG-coA reductase degradation 1 homolog
RING-type E3 ubiquitin transferase synoviolin
synovial apoptosis inhibitor 1, synoviolin
NP_115807.1
NP_757385.1
XP_011543605.1
XP_047283667.1
XP_047283668.1
XP_047283669.1
XP_054226165.1
XP_054226166.1
XP_054226167.1
XP_054226168.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029713.2 RefSeqGene

    Range
    5000..12240
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_032431.3 → NP_115807.1  E3 ubiquitin-protein ligase synoviolin isoform a

    See identical proteins and their annotated locations for NP_115807.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (a).
    Source sequence(s)
    AA864844, AL834262, BC030530
    Consensus CDS
    CCDS8097.1
    UniProtKB/TrEMBL
    B3KX82
    Related
    ENSP00000294256.8, ENST00000294256.12
    Conserved Domains (3) summary
    COG5243
    Location:10 → 333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:527 → 610
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289 → 330
    zf-RING_2; Ring finger domain

  2. NM_172230.3 → NP_757385.1  E3 ubiquitin-protein ligase synoviolin isoform b

    See identical proteins and their annotated locations for NP_757385.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses a different splice site than variant 1 and encodes the longer isoform (b).
    Source sequence(s)
    AA864844, AL834262, BC030530
    Consensus CDS
    CCDS31605.1
    UniProtKB/Swiss-Prot
    Q86TM6, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3
    UniProtKB/TrEMBL
    B3KX82
    Related
    ENSP00000366395.3, ENST00000377190.8
    Conserved Domains (3) summary
    COG5243
    Location:10 → 333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:528 → 611
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289 → 330
    zf-RING_2; Ring finger domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    65127279..65134519 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047427713.1 → XP_047283669.1  E3 ubiquitin-protein ligase synoviolin isoform X4

    Related
    ENSP00000436984.1, ENST00000526060.5

  2. XM_047427712.1 → XP_047283668.1  E3 ubiquitin-protein ligase synoviolin isoform X2

  3. XM_011545303.4 → XP_011543605.1  E3 ubiquitin-protein ligase synoviolin isoform X3

    See identical proteins and their annotated locations for XP_011543605.1

    UniProtKB/Swiss-Prot
    Q86TM6, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3
    UniProtKB/TrEMBL
    B3KX82
    Conserved Domains (3) summary
    COG5243
    Location:10 → 333
    HRD1; HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
    pfam08619
    Location:528 → 611
    Nha1_C; Alkali metal cation/H+ antiporter Nha1 C terminus
    pfam13639
    Location:289 → 330
    zf-RING_2; Ring finger domain

  4. XM_047427711.1 → XP_047283667.1  E3 ubiquitin-protein ligase synoviolin isoform X1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    65120558..65127829 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370193.1 → XP_054226168.1  E3 ubiquitin-protein ligase synoviolin isoform X4

  2. XM_054370192.1 → XP_054226167.1  E3 ubiquitin-protein ligase synoviolin isoform X3

    UniProtKB/Swiss-Prot
    Q86TM6, Q8N3K3, Q8N6E8, Q96JL5, Q96PK3

  3. XM_054370191.1 → XP_054226166.1  E3 ubiquitin-protein ligase synoviolin isoform X2

  4. XM_054370190.1 → XP_054226165.1  E3 ubiquitin-protein ligase synoviolin isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q86TM6.2 GenPept UniProtKB/Swiss-Prot:Q86TM6

Gene LinkOut

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