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	9711
Gene name	Rubicon autophagy regulator
Gene symbol	RUBCN
Synonyms (NCBI Gene)	KIAA0226RUBICONSCAR15
Chromosome	3
Chromosome location	3q29
Summary	The protein encoded by this gene is a negative regulator of autophagy and endocytic trafficking and controls endosome maturation. This protein contains two conserved domains, an N-terminal RUN domain and a C-terminal DUF4206 domain. The RUN domain is invo

Show/Hide all (4)

SNP ID	Visualize variation	Clinical significance	Consequence
rs115638090	C>T	Conflicting-interpretations-of-pathogenicity	5 prime UTR variant, missense variant, coding sequence variant
rs587777235	G>-	Pathogenic	Coding sequence variant, frameshift variant
rs767982852	T>C	Pathogenic, uncertain-significance	Coding sequence variant, missense variant
rs1114167292	C>T	Pathogenic, uncertain-significance	Missense variant, 5 prime UTR variant, coding sequence variant

Show/Hide all (25)

miRTarBase ID	miRNA	Experiments	Reference
MIRT474834	hsa-miR-15b-5p	PAR-CLIP	23592263
MIRT474833	hsa-miR-497-5p	PAR-CLIP	23592263
MIRT474832	hsa-miR-195-5p	PAR-CLIP	23592263
MIRT474831	hsa-miR-16-5p	PAR-CLIP	23592263
MIRT474830	hsa-miR-6838-5p	PAR-CLIP	23592263
MIRT474829	hsa-miR-424-5p	PAR-CLIP	23592263
MIRT474828	hsa-miR-15a-5p	PAR-CLIP	23592263
MIRT474827	hsa-miR-6768-3p	PAR-CLIP	23592263
MIRT474826	hsa-miR-6165	PAR-CLIP	23592263
MIRT474825	hsa-miR-922	PAR-CLIP	23592263
MIRT474824	hsa-miR-214-3p	PAR-CLIP	23592263
MIRT474823	hsa-miR-3619-5p	PAR-CLIP	23592263
MIRT474822	hsa-miR-761	PAR-CLIP	23592263
MIRT474821	hsa-miR-4768-3p	PAR-CLIP	23592263
MIRT474820	hsa-miR-539-5p	PAR-CLIP	23592263
MIRT474819	hsa-miR-6134	PAR-CLIP	23592263
MIRT474818	hsa-miR-4722-5p	PAR-CLIP	23592263
MIRT474817	hsa-miR-876-3p	PAR-CLIP	23592263
MIRT474816	hsa-miR-380-5p	PAR-CLIP	23592263
MIRT474815	hsa-miR-563	PAR-CLIP	23592263
MIRT474814	hsa-miR-1273g-5p	PAR-CLIP	23592263
MIRT474813	hsa-miR-4291	PAR-CLIP	23592263
MIRT474812	hsa-miR-580-3p	PAR-CLIP	23592263
MIRT440396	hsa-miR-543	HITS-CLIP	24374217
MIRT440396	hsa-miR-543	HITS-CLIP	24374217

Show/Hide all (26)

GO ID	Ontology	Definition	Evidence	Reference
GO:0002376	Process	Immune system process	IEA
GO:0005515	Function	Protein binding	IPI	19270696, 20562859, 21062745, 22493499, 23954414, 24034250, 25594178, 32296183, 33961781, 34386498, 35271311, 35512704
GO:0005654	Component	Nucleoplasm	IDA
GO:0005764	Component	Lysosome	IEA
GO:0005768	Component	Endosome	IEA
GO:0005769	Component	Early endosome	IBA
GO:0005769	Component	Early endosome	IDA	19270696
GO:0005769	Component	Early endosome	IEA
GO:0005770	Component	Late endosome	IBA
GO:0005770	Component	Late endosome	IDA	19270696
GO:0005770	Component	Late endosome	IEA
GO:0005794	Component	Golgi apparatus	IDA	19270696
GO:0005829	Component	Cytosol	IDA
GO:0006897	Process	Endocytosis	IEA
GO:0006909	Process	Phagocytosis	IEA
GO:0006914	Process	Autophagy	IEA
GO:0010507	Process	Negative regulation of autophagy	IMP	19270696
GO:0045806	Process	Negative regulation of endocytosis	IBA
GO:0045806	Process	Negative regulation of endocytosis	IMP	19270696
GO:0051898	Process	Negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IDA	21062745
GO:0071985	Process	Multivesicular body sorting pathway	TAS	21118109
GO:0141039	Function	Phosphatidylinositol 3-kinase inhibitor activity	IDA	21062745
GO:1901097	Process	Negative regulation of autophagosome maturation	IBA
GO:1901097	Process	Negative regulation of autophagosome maturation	IMP	21062745
GO:1901097	Process	Negative regulation of autophagosome maturation	TAS	21118109
GO:1901981	Function	Phosphatidylinositol phosphate binding	IBA

MIM	HGNC	e!Ensembl
613516	28991	ENSG00000145016

Q92622

Protein name

Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (Rubicon) (Beclin-1 associated RUN domain containing protein) (Baron)

Protein function

Inhibits PIK3C3 activity; under basal conditions negatively regulates PI3K complex II (PI3KC3-C2) function in autophagy. Negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process.

PDB

6WCW

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF02759	RUN	56 → 181	RUN domain	Family
PF13901	zf-RING_9	737 → 937	Putative zinc-RING and/or ribbon	Domain

Sequence

MRPEGAGMELGGGEERLPEESRREHWQLLGNLKTTVEGLVSTNSPNVWSKYGGLERLCRD
MQSILYHGLIRDQACRRQTDYWQFVKDIRWLSPHSALHVEKFISVHENDQSSADGASERA
VAELWLQHSLQYHCLSAQLRPLLGDRQYIRKFYTDAAFLLSDAHVTAMLQCLEAVEQNNP
RLLAQIDASMFARKHESPLLVTKSQSLTALPSSTYTPPNSYAQHSYFGSFSSLHQSVPNN
GSERRSTSFPLSGPPRKPQESRGHVSPAEDQTIQAPPVSVSALARDSPLTPNEMSSSTLT
SPIEASWVSSQNDSPGDASEGPEYLAIGNLDPRGRTASCQSHSSNAESSSSNLFSSSSSQ
KPDSAASSLGDQEGGGESQLSSVLRRSSFSEGQTLTVTSGAKKSHIRSHSDTSIASRGAP
ESCNDKAKLRGPLPYSGQSSEVSTPSSLYMEYEGGRYLCSGEGMFRRPSEGQSLISYLSE
QDFGSCADLEKENAHFSISESLIAAIELMKCNMMSQCLEEEEVEEEDSDREIQELKQKIR
LRRQQIRTKNLLPMYQEAEHGSFRVTSSSSQFSSRDSAQLSDSGSADEVDEFEIQDADIR
RNTASSSKSFVSSQSFSHCFLHSTSAEAVAMGLLKQFEGMQLPAASELEWLVPEHDAPQK
LLPIPDSLPISPDDGQHADIYKLRIRVRGNLEWAPPRPQIIFNVHPAPTRKIAVAKQNYR
CAGCGIRTDPDYIKRLRYCEYLGKYFCQCCHENAQMAIPSRVLRKWDFSKYYVSNFSKDL
LIKIWNDPLFNVQDINSALYRKVKLLNQVRLLRVQLCHMKNMFKTCRLAKELLDSFDTVP
GHLTEDLHLYSLNDLTATRKGELGPRLAELTRAGATHVERCMLCQAKGFICEFCQNEDDI
IFPFELHKCRTCEECKACYHKACFKSGSCPRCERLQARREALARQSLESYLSDYEEEPAE
ALALEAAVLEAT

Sequence length

972

Interactions

View interactions

	KEGG
	Autophagy - animal

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)

Show/Hide Causal Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autosomal recessive spinocerebellar ataxia 15	Pathogenic; Likely pathogenic	rs587777235, rs2474191525, rs375400873	RCV000106316 RCV003234625 RCV003584026	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spinocerebellar ataxia type 15/16	Likely pathogenic	rs746764220	RCV004515772	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (12)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
ATAXIA, SPINOCEREBELLAR	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CEREBELLAR ATAXIA, EPILEPSY, INTELLECTUAL DISABILITY SYNDROME DUE TO RUN AND CYSTEINE RICH DOMAIN CONTAINING BECLIN 1 INTERACTING PROTEIN DEFICIENCY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTOSOMAL RECESSIVE CEREBELLAR ATAXIA-EPILEPSY-INTELLECTUAL DISABILITY SYNDROME DUE TO RUBCN DEFICIENCY	—	Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GLOBAL DEVELOPMENTAL DELAY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTELLECTUAL DISABILITY	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NYSTAGMUS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RUBCN-related disorder	Likely benign; Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Conflicting classifications of pathogenicity	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA 15	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 15	—	HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIAS	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (31)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Anaplasia	Anaplasia	BEFREE	31116585		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ataxia, Spinocerebellar	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Atrophy	Atrophy	Pubtator	32450808	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Autosomal recessive cerebellar ataxia-epilepsy-intellectual disability syndrome due to RUBCN deficiency	Cerebellar Ataxia, Epilepsy, Mental Retardation	Orphanet			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	33650674	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37898101	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cholestasis	Cholelithiasis	Pubtator	32001325	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Clumsiness - motor delay	Motor delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	36476132	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetic Nephropathies	Diabetic neuropathy	Pubtator	36476132	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Dysarthria	Dysarthria	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Flexion contracture - elbow	Elbow flexion contracture	CLINVAR_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gross motor development delay	Developmental delay	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Hepatitis B	Hepatitis b	Pubtator	28392573	Stimulate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Kidney Neoplasms	Kidney neoplasm	Pubtator	37898101	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Liver Diseases	Liver disease	Pubtator	32001325	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Lupus Erythematosus, Systemic	Lupus Erythematosus	BEFREE	30755075		★★★★★ ★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nystagmus	Nystagmus	HPO_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar Ataxia Type 1	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 2	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 4	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 5	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 6 (disorder)	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Spinocerebellar Ataxia Type 7	Spinocerebellar Ataxia	CTD_human_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 15	Spinocerebellar Ataxia	GENOMICS_ENGLAND_DG	20826435		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 15	Spinocerebellar Ataxia	ORPHANET_DG	23728897		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPINOCEREBELLAR ATAXIA, AUTOSOMAL RECESSIVE 15	Spinocerebellar Ataxia	CLINVAR_DG			★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Spinocerebellar Ataxias	Spinocerebellar ataxia	Pubtator	32450808	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

RUBCN (rubicon autophagy regulator)