Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
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]

Show/Hide all (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
rs727503764	AGTG>-	Pathogenic	Downstream transcript variant, splice donor variant, coding sequence variant, genic downstream transcript variant, frameshift variant, intron variant
rs727503765	G>T	Pathogenic	Stop gained, synonymous variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs730880329	->GGCG	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs730880330	->GACGAGG	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, genic downstream transcript variant
rs780854072	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained, genic downstream transcript variant
rs1017046170	G>A,C	Pathogenic	Genic downstream transcript variant, splice donor variant
rs1342598444	G>A	Pathogenic	Missense variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant, non coding transcript variant
rs1555787599	G>T	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, missense variant
rs1555787903	G>T	Likely-pathogenic	Genic downstream transcript variant, splice donor variant
rs1568554654	C>T	Pathogenic	Non coding transcript variant, coding sequence variant, genic downstream transcript variant, stop gained, 5 prime UTR variant

Show/Hide all (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
MIRT1294131	hsa-miR-2467-3p	CLIP-seq
MIRT1294132	hsa-miR-3175	CLIP-seq
MIRT1294133	hsa-miR-4257	CLIP-seq
MIRT1294134	hsa-miR-4269	CLIP-seq
MIRT1294135	hsa-miR-4300	CLIP-seq
MIRT1294136	hsa-miR-4306	CLIP-seq
MIRT1294137	hsa-miR-4307	CLIP-seq
MIRT1294138	hsa-miR-4477b	CLIP-seq
MIRT1294139	hsa-miR-4505	CLIP-seq
MIRT1294140	hsa-miR-4514	CLIP-seq
MIRT1294141	hsa-miR-4644	CLIP-seq
MIRT1294142	hsa-miR-4692	CLIP-seq
MIRT1294143	hsa-miR-4731-5p	CLIP-seq
MIRT1294144	hsa-miR-4742-5p	CLIP-seq
MIRT1294145	hsa-miR-615-5p	CLIP-seq
MIRT1294146	hsa-miR-920	CLIP-seq
MIRT2087452	hsa-miR-1972	CLIP-seq
MIRT2087453	hsa-miR-4650-5p	CLIP-seq
MIRT2087454	hsa-miR-548an	CLIP-seq
MIRT2608749	hsa-miR-2467-5p	CLIP-seq
MIRT2608750	hsa-miR-3176	CLIP-seq
MIRT2608751	hsa-miR-377	CLIP-seq
MIRT2608752	hsa-miR-3922-3p	CLIP-seq
MIRT2608753	hsa-miR-3922-5p	CLIP-seq
MIRT1294137	hsa-miR-4307	CLIP-seq
MIRT2608754	hsa-miR-4435	CLIP-seq
MIRT2608755	hsa-miR-4489	CLIP-seq
MIRT2608756	hsa-miR-4708-3p	CLIP-seq
MIRT2608757	hsa-miR-4757-5p	CLIP-seq
MIRT2689390	hsa-miR-1323	CLIP-seq
MIRT2689391	hsa-miR-1343	CLIP-seq
MIRT2689392	hsa-miR-139-3p	CLIP-seq
MIRT2689393	hsa-miR-149	CLIP-seq
MIRT2689394	hsa-miR-218	CLIP-seq
MIRT1294131	hsa-miR-2467-3p	CLIP-seq
MIRT2608749	hsa-miR-2467-5p	CLIP-seq
MIRT2689395	hsa-miR-3158-5p	CLIP-seq
MIRT2689396	hsa-miR-3160-5p	CLIP-seq
MIRT2608750	hsa-miR-3176	CLIP-seq
MIRT2689397	hsa-miR-3667-3p	CLIP-seq
MIRT2689398	hsa-miR-3678-3p	CLIP-seq
MIRT2608751	hsa-miR-377	CLIP-seq
MIRT2608752	hsa-miR-3922-3p	CLIP-seq
MIRT2608753	hsa-miR-3922-5p	CLIP-seq
MIRT2689399	hsa-miR-3941	CLIP-seq
MIRT2689400	hsa-miR-3944-5p	CLIP-seq
MIRT1294137	hsa-miR-4307	CLIP-seq
MIRT2689401	hsa-miR-4419a	CLIP-seq
MIRT2608754	hsa-miR-4435	CLIP-seq
MIRT2689402	hsa-miR-4438	CLIP-seq
MIRT1294138	hsa-miR-4477b	CLIP-seq
MIRT2608755	hsa-miR-4489	CLIP-seq
MIRT1294139	hsa-miR-4505	CLIP-seq
MIRT2689403	hsa-miR-4510	CLIP-seq
MIRT2689404	hsa-miR-4539	CLIP-seq
MIRT2689405	hsa-miR-466	CLIP-seq
MIRT2689406	hsa-miR-4672	CLIP-seq
MIRT2689407	hsa-miR-4675	CLIP-seq
MIRT2608756	hsa-miR-4708-3p	CLIP-seq
MIRT1294143	hsa-miR-4731-5p	CLIP-seq
MIRT2689408	hsa-miR-4741	CLIP-seq
MIRT2608757	hsa-miR-4757-5p	CLIP-seq
MIRT2689409	hsa-miR-492	CLIP-seq
MIRT2689410	hsa-miR-548a-3p	CLIP-seq
MIRT2689411	hsa-miR-548e	CLIP-seq
MIRT2689412	hsa-miR-548f	CLIP-seq
MIRT2689413	hsa-miR-548g	CLIP-seq
MIRT2689414	hsa-miR-548o	CLIP-seq
MIRT2689415	hsa-miR-607	CLIP-seq
MIRT2689416	hsa-miR-636	CLIP-seq
MIRT2689417	hsa-miR-760	CLIP-seq

Show/Hide all (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
GO:0004842	Function	Ubiquitin-protein transferase activity	IEA
GO:0005515	Function	Protein binding	IPI	16083853, 16643902, 17006537, 17449468, 18711448, 19549727, 20098747, 21455180, 21455181, 21709223, 21811235, 21903422, 22430200, 22791023, 23032186, 23088713, 24141947, 25260751, 25416956, 26871637, 28514442, 29892012, 29997244, 30561431, 32296183, 32814053, 33961781, 36179048
GO:0005829	Component	Cytosol	TAS
GO:0008270	Function	Zinc ion binding	IEA
GO:0010604	Process	Positive regulation of macromolecule metabolic process	IEA
GO:0016567	Process	Protein ubiquitination	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0032088	Process	Negative regulation of NF-kappaB transcription factor activity	IDA	17449468
GO:0042742	Process	Defense response to bacterium	IMP	28481331
GO:0042802	Function	Identical protein binding	IPI	25416956, 30561431
GO:0043065	Process	Positive regulation of apoptotic process	IEA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IBA
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IDA	19136968, 21455173
GO:0043123	Process	Positive regulation of canonical NF-kappaB signal transduction	IEA
GO:0043130	Function	Ubiquitin binding	IBA
GO:0043130	Function	Ubiquitin binding	IDA	21455181
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IBA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IMP	17449468
GO:0045893	Process	Positive regulation of DNA-templated transcription	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0050852	Process	T cell receptor signaling pathway	IDA	20005846
GO:0051092	Process	Positive regulation of NF-kappaB transcription factor activity	IDA	19136968
GO:0060546	Process	Negative regulation of necroptotic process	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IEA
GO:0071797	Component	LUBAC complex	IBA
GO:0071797	Component	LUBAC complex	IDA	17006537, 21455173, 21455180, 21455181, 24726323, 27523608, 28481331
GO:0071797	Component	LUBAC complex	IEA
GO:0071797	Component	LUBAC complex	IPI	21455180
GO:0080090	Process	Regulation of primary metabolic process	IEA
GO:0097039	Process	Protein linear polyubiquitination	IBA
GO:0097039	Process	Protein linear polyubiquitination	IDA	21455173, 21455180, 21455181, 23453807
GO:0140311	Function	Protein sequestering activity	IDA	16083853
GO:1901224	Process	Positive regulation of non-canonical NF-kappaB signal transduction	IEA
GO:1990757	Function	Ubiquitin ligase activator activity	IEA
GO:2001238	Process	Positive regulation of extrinsic apoptotic signaling pathway	IEA

MIM	HGNC	e!Ensembl
610924	15864	ENSG00000125826

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
LHTFCRECLQGTIRNSQEAEVSCPFIDNTYSCSGKLLEREIKALLTPEDYQRFLDLGISI
AENRSAFSYHCKTPDCKGWCFFEDDVNEFTCPVCFHVNCLLCKAIHEQMNCKEYQEDLAL
RAQNDVAARQTTEMLKVMLQQGEAMRCPQCQIVVQKKDGCDWIRCTVCHTEICWVTKGPR
WGPGGPGDTSGGCRCRVNGIPCHPSCQNCH

Sequence length

510

Interactions

View interactions

	KEGG		Reactome
	Necroptosis NOD-like receptor signaling pathway Shigellosis		Regulation of TNFR1 signaling TNFR1-induced NFkappaB signaling pathway Antigen processing: Ubiquitination & Proteasome degradation

473

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Polyglucosan body myopathy 1 with immunodeficiency	Pathogenic	rs727503762, rs727503763, rs2122245690	RCV001840044 RCV001840045 RCV002260922
Polyglucosan body myopathy 1 without immunodeficiency	Likely pathogenic; Pathogenic	rs2122268166, rs2122349615, rs566912235, rs730880329, rs587777561, rs730880330, rs2122268456, rs2122348874	RCV002264818 RCV002264819 RCV001840047 RCV001840048 RCV001840049 RCV001840050 RCV002260925 RCV002260926
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 RCV001542620 RCV001898286 RCV000128836 RCV000128837 RCV000128838 RCV002477341 RCV000128840 RCV000128841 RCV002250289 RCV003094103 RCV005025746 RCV002796901 RCV002881014 RCV003014986 RCV003234840 RCV003585503 RCV003585517 RCV003584131 RCV001380133 RCV000703630 RCV000812501 RCV000815854 RCV001197353 RCV001233660 RCV001283769
See cases	Likely pathogenic; Pathogenic	rs2016260522	RCV002252804

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Clear cell carcinoma of kidney	Uncertain significance	rs780470011	RCV005924274
Gastric cancer	Likely benign	rs1470415932	RCV005931273
Glycogen storage disease, type IV	Conflicting classifications of pathogenicity	rs1555787599	RCV000590988
Melanoma	Uncertain significance	rs201470953	RCV005900345
RBCK1-related disorder	Likely benign; Conflicting classifications of pathogenicity; Uncertain significance; Benign	rs1330864432, rs1169837697, rs377605009, rs148091459, rs201030033, rs149541936, rs149008463, rs776856644, rs149038161, rs993862197	RCV003967161 RCV003967211 RCV003952866 RCV003953194 RCV004757285 RCV003910648 RCV003950537 RCV003913075 RCV003905996 RCV003898063

Show/Hide Text Mining Associations (31)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Adenocarcinoma of Lung	Associate	31847905
Breast Neoplasms	Associate	29763465, 36473847
Breast Neoplasms	Stimulate	36280829
Carcinoma Hepatocellular	Associate	38214606
Carcinoma Renal Cell	Associate	34795663
Cardiomyopathies	Associate	23798481, 36672924
Cardiomyopathy Dilated	Associate	36672924, 38329383
Cognition Disorders	Stimulate	33413275
Cognition Disorders	Associate	33413275
Colorectal Neoplasms	Associate	36941538
Disease	Associate	29260357
Distal myopathy Nonaka type	Associate	29260357
Endocrine System Diseases	Associate	36280829
Fasciculation	Associate	33413275
Glycogen Storage Disease Type IV	Associate	23104095, 26008899
Heart Diseases	Associate	29260357
Hereditary Autoinflammatory Diseases	Associate	23104095, 26008899, 29260357, 32122970
Hypoxia	Associate	36473847
Immune System Diseases	Associate	29260357
Immunologic Deficiency Syndromes	Associate	23104095, 29260357, 38329383
Infections	Associate	26008899
Inflammation	Associate	17449468, 35906541, 38329383
Leukoencephalopathies	Associate	33413275
Muscle Weakness	Associate	23798481, 38329383
Muscular Diseases	Associate	29260357, 38329383
Neoplasm Metastasis	Associate	31847905
Neoplasms	Associate	19277210, 34795663, 38002938
Neoplasms	Stimulate	29763465, 38214606
Nervous System Diseases	Associate	35017290
Polyglucosan Body Disease Adult Form	Associate	23798481, 29260357, 33413275, 35017290
Triple Negative Breast Neoplasms	Inhibit	36280829

RBCK1 (RANBP2-type and C3HC4-type zinc finger containing 1)