Gene Gene information from NCBI Gene database.
Entrez ID 10616
Gene name RANBP2-type and C3HC4-type zinc finger containing 1
Gene symbol RBCK1
Synonyms (NCBI Gene)
C20orf18HOIL-1HOIL1PBMEIPGBM1RBCK2RNF54UBCE7IP3XAP3XAP4ZRANB4
Chromosome 20
Chromosome location 20p13
Summary The protein encoded by this gene is similar to mouse UIP28/UbcM4 interacting protein. Alternative splicing has been observed at this locus, resulting in distinct isoforms. [provided by RefSeq, Jul 2008]
SNPs SNP information provided by dbSNP.
15
SNP ID Visualize variation Clinical significance Consequence
rs377605009 A>G Conflicting-interpretations-of-pathogenicity Downstream transcript variant, missense variant, genic downstream transcript variant, coding sequence variant, intron variant, non coding transcript variant
rs566912235 A>G Pathogenic Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant
rs587777561 C>T Pathogenic Downstream transcript variant, stop gained, coding sequence variant, genic downstream transcript variant, intron variant, non coding transcript variant
rs727503762 C>T Pathogenic Stop gained, synonymous variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs727503763 CT>- Pathogenic 5 prime UTR variant, coding sequence variant, frameshift variant, intron variant, non coding transcript variant
miRNA miRNA information provided by mirtarbase database.
76
miRTarBase ID miRNA Experiments Reference
MIRT019076 hsa-miR-335-5p Microarray 18185580
MIRT023193 hsa-miR-124-3p Microarray 18668037
MIRT025392 hsa-miR-34a-5p Proteomics 21566225
MIRT1294129 hsa-miR-185 CLIP-seq
MIRT1294130 hsa-miR-1909 CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
40
GO ID Ontology Definition Evidence Reference
GO:0000209 Process Protein polyubiquitination IDA 12629548, 17006537
GO:0000209 Process Protein polyubiquitination IEA
GO:0003713 Function Transcription coactivator activity IDA 20103625
GO:0004842 Function Ubiquitin-protein transferase activity IBA
GO:0004842 Function Ubiquitin-protein transferase activity IDA 12629548, 17006537
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
610924 15864 ENSG00000125826
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9BYM8
Protein name RanBP-type and C3HC4-type zinc finger-containing protein 1 (EC 2.3.2.31) (HBV-associated factor 4) (Heme-oxidized IRP2 ubiquitin ligase 1) (HOIL-1) (Hepatitis B virus X-associated protein 4) (RING finger protein 54) (RING-type E3 ubiquitin transferase HOI
Protein function E3 ubiquitin-protein ligase, which accepts ubiquitin from specific E2 ubiquitin-conjugating enzymes, such as UBE2L3/UBCM4, and then transfers it to substrates (PubMed:12629548, PubMed:17449468, PubMed:18711448). Functions as an E3 ligase for oxi
PDB 2CRC , 2LGY , 4DBG , 7V8E , 7YUI , 7YUJ , 8BVL , 8EAZ , 8K6Q , 9EGV , 9EGW
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13445 zf-RING_UBOX 282 324 RING-type zinc-finger Domain
PF01485 IBR 351 411 IBR domain, a half RING-finger domain Domain
Sequence
MDEKTKKAEEMALSLTRAVAGGDEQVAMKCAIWLAEQRVPLSVQLKPEVSPTQDIRLWVS
VEDAQMHTVTIWLTVRPDMTVASLKDMVFLDYGFPPVLQQWVIGQRLARDQETLHSHGVR
QNGDSAYLYLLSARNTSLNPQELQRERQLRMLEDLGFKDLTLQPRGPLEPGPPKPGVPQE
PGRGQPDAVPEPPPVGWQCPGCTFINKPTRPGCEMCCRARPEAYQVPASYQPDEEERARL
AGEEEALRQYQQRKQQQQEGNYLQHVQLDQRSLVLNTEPAECPVCYSVLAPGEAVVLREC
LHTFCRECLQGTIRNSQEAEVSCP
FIDNTYSCSGKLLEREIKALLTPEDYQRFLDLGISI
AENRSAFSYHCKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMNC
KEYQEDLAL
RAQNDVAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGCDWIRCTVCHTEICWVTKGPR
WGPGGPGDTSGGCRCRVNGIPCHPSCQNCH
Sequence length 510
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Necroptosis
NOD-like receptor signaling pathway
Shigellosis
  Regulation of TNFR1 signaling
TNFR1-induced NFkappaB signaling pathway
Antigen processing: Ubiquitination & Proteasome degradation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
13
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Polyglucosan body myopathy 1 with immunodeficiency Pathogenic rs727503762, rs727503763, rs2122245690 RCV001840044
RCV001840045
RCV002260922
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Polyglucosan body myopathy 1 without immunodeficiency Likely pathogenic; Pathogenic rs2122268166, rs2122349615, rs566912235, rs730880329, rs587777561, rs730880330, rs2122268456, rs2122348874 RCV002264818
RCV002264819
RCV001840047
RCV001840048
RCV001840049
View all (3 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Polyglucosan body myopathy type 1 Pathogenic; Likely pathogenic rs1487503835, rs2122245228, rs2122281705, rs2122333654, rs2122268166, rs2122349615, rs2016261486, rs727503764, rs566912235, rs727503765, rs730880329, rs587777561, rs730880330, rs2122282189, rs2016260522
View all (14 more)
RCV001382927
RCV001389444
RCV001385035
RCV001865947
RCV001542619
View all (25 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
AUTOINFLAMMATORY SYNDROME WITH PYOGENIC BACTERIAL INFECTION AND AMYLOPECTINOSIS CTD, Disgenet, Orphanet
CTD, Disgenet, Orphanet
CTD, Disgenet, Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CARDIOMEGALY CTD
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney Uncertain significance ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Autoimmune Diseases Autoimmune Diseases BEFREE 29695863
★☆☆☆☆
Found in Text Mining only
Branchio-Oto-Renal Syndrome Branchiootorenal Syndrome BEFREE 20956555
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 20103625
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 29763465, 36473847 Associate
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 36280829 Stimulate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 38214606 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Renal Cell Renal cell carcinoma Pubtator 34795663 Associate
★☆☆☆☆
Found in Text Mining only
Cardiomyopathies Cardiomyopathy BEFREE 23798481, 23995275
★☆☆☆☆
Found in Text Mining only
Cardiomyopathies Cardiomyopathy Pubtator 23798481, 36672924 Associate
★☆☆☆☆
Found in Text Mining only
Cardiomyopathy Dilated Dilated cardiomyopathy Pubtator 36672924, 38329383 Associate
★☆☆☆☆
Found in Text Mining only