DENND3 (DENN domain containing 3)

Gene

• Entrez ID: 22898
• Gene name: DENN domain containing 3
• Gene symbol: DENND3
• Synonyms (NCBI Gene): -
• Chromosome: 8
• Chromosome location: 8q24.3

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519052	G>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, non coding transcript variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT019167	hsa-miR-335-5p	Microarray	18185580
MIRT932369	hsa-miR-1255a	CLIP-seq
MIRT932370	hsa-miR-1255b	CLIP-seq
MIRT932371	hsa-miR-1913	CLIP-seq
MIRT932372	hsa-miR-324-3p	CLIP-seq
MIRT932373	hsa-miR-3607-5p	CLIP-seq
MIRT932374	hsa-miR-365	CLIP-seq
MIRT932375	hsa-miR-4330	CLIP-seq
MIRT932376	hsa-miR-4471	CLIP-seq
MIRT932377	hsa-miR-4639-3p	CLIP-seq
MIRT932378	hsa-miR-4717-5p	CLIP-seq
MIRT932379	hsa-miR-4768-5p	CLIP-seq
MIRT932380	hsa-miR-487a	CLIP-seq
MIRT932381	hsa-miR-499a-5p	CLIP-seq
MIRT932382	hsa-miR-520d-5p	CLIP-seq
MIRT932383	hsa-miR-524-5p	CLIP-seq
MIRT932384	hsa-miR-542-5p	CLIP-seq
MIRT932376	hsa-miR-4471	CLIP-seq
MIRT932384	hsa-miR-542-5p	CLIP-seq
MIRT1976074	hsa-miR-3612	CLIP-seq
MIRT1976075	hsa-miR-3614-5p	CLIP-seq
MIRT1976076	hsa-miR-4418	CLIP-seq
MIRT1976077	hsa-miR-4436b-5p	CLIP-seq
MIRT1976078	hsa-miR-4443	CLIP-seq
MIRT932376	hsa-miR-4471	CLIP-seq
MIRT1976079	hsa-miR-4771	CLIP-seq
MIRT1976080	hsa-miR-509-3-5p	CLIP-seq
MIRT1976081	hsa-miR-509-5p	CLIP-seq
MIRT1976082	hsa-miR-512-5p	CLIP-seq
MIRT1976083	hsa-miR-516b	CLIP-seq
MIRT932384	hsa-miR-542-5p	CLIP-seq
MIRT1976084	hsa-miR-650	CLIP-seq
MIRT932369	hsa-miR-1255a	CLIP-seq
MIRT932370	hsa-miR-1255b	CLIP-seq
MIRT2386838	hsa-miR-1275	CLIP-seq
MIRT2386839	hsa-miR-3189-3p	CLIP-seq
MIRT2386840	hsa-miR-329	CLIP-seq
MIRT2386841	hsa-miR-3605-5p	CLIP-seq
MIRT2386842	hsa-miR-362-3p	CLIP-seq
MIRT2386843	hsa-miR-4324	CLIP-seq
MIRT2386844	hsa-miR-4329	CLIP-seq
MIRT2386845	hsa-miR-4525	CLIP-seq
MIRT2386846	hsa-miR-4665-5p	CLIP-seq
MIRT2386847	hsa-miR-4723-5p	CLIP-seq
MIRT2386848	hsa-miR-625	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005085	Function	Guanyl-nucleotide exchange factor activity	IDA	20937701
GO:0005085	Function	Guanyl-nucleotide exchange factor activity	IEA
GO:0005085	Function	Guanyl-nucleotide exchange factor activity	TAS
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0008333	Process	Endosome to lysosome transport	ISS
GO:0030163	Process	Protein catabolic process	ISS
GO:0031410	Component	Cytoplasmic vesicle	IBA
GO:0032483	Process	Regulation of Rab protein signal transduction	IBA

Other IDs

• MIM: 617503
• HGNC: 29134
• e!Ensembl: ENSG00000105339

Protein

• UniProt ID: A2RUS2
• Protein name: DENN domain-containing protein 3
• Protein function: Guanine nucleotide exchange factor (GEF) activating RAB12. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB12 into its active GTP-bound form (PubMed:20937701). Regulates autophagy in response to starvation through RAB12 act
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02141	DENN	105 → 291	DENN (AEX-3) domain	Family
  PF19056	WD40_2	893 → 998		Repeat

• Sequence:

  MRSLRKKREKPRPEQWKGLPGPPRAPEPEDVAVPGGVDLLTLPQLCFPGGVCVATEPKED
  CVHFLVLTDVCGNRTYGVVAQYYRPLHDEYCFYNGKTHRECPGCFVPFAVCVVSRFPYYN
  SLKDCLSCLLALLKPCKDFEVDSHIKDFAAKLSLIPSPPPGPLHLVFNMKSLQIVLPARA
  DPESPILDLDLHLPLLCFRPEKVLQILTCILTEQRIVFFSSDWALLTLVTECFMAYLYPL
  QWQHPFVPILSDQMLDFVMAPTSFLMGCHLDHFEEVSKEADGLVLINIDHGSITYSKSTD
  DNVDIPDVPLLAAQTFIQRVQSLQLHHELHAAHLLSSTDLKEGRAHRRSWQQKLNCQIQQ
  TTLQLLVSIFRDVKNHLNYEHRVFNSEEFLKTRAPGDHQFYKQVLDTYMFHSFLKARLNR
  RMDAFAQMDLDTQSEEDRINGMLLSPRRPTVEKRASRKSSHLHVTHRRMVVSMPNLQDIA
  MPELAPRNSSLRLTDTAGCRGSSAVLNVTPKSPYTFKIPEIHFPLESKCVQAYHAHFVSM
  LSEAMCFLAPDNSLLLARYLYLRGLVYLMQGQLLNALLDFQNLYKTDIRIFPTDLVKRTV
  ESMSAPEWEGAEQAPELMRLISEILDKPHEASKLDDHVKKFKLPKKHMQLGDFMKRVQES
  GIVKDASIIHRLFEALTVGQEKQIDPETFKDFYNCWKETEAEAQEVSLPWLVMEHLDKNE
  CVCKLSSSVKTNLGVGKIAMTQKRLFLLTEGRPGYLEISTFRNIEEVRRTTTTFLLRRIP
  TLKIRVASKKEVFEANLKTECDLWHLMVKEMWAGKKLADDHKDPHYVQQALTNVLLMDAV
  VGTLQSPGAIYAASKLSYFDKMSNEMPMTLPETTLETLKHKINPSAGEAFPQAVDVLLYT
  PGHLDPAEKVEDAHPKLWCALSEGKVTVFNASSWTIHQHSFKVGTAKVNCMVMADQNQVW
  VGSEDSVIYIINVHSMSCNKQLTAHCSSVTDLIVQDGQEAPSNVYSCSMDGMVLVWNVST
  LQVTSRFQLPRGGLTSIRLHGGRLWCCTGNSIMVMKMNGSLHQELKIEENFKDTSTSFLA
  FQLLPEEEQLWAACAGRSEVYIWSLKDLAQPPQRVPLEDCSEINCMIRVKKQVWVGSRGL
  GQGTPKGKIYVIDAERKTVEKELVAHMDTVRTLCSAEDRYVLSGSGREEGKVAIWKGE

• Sequence length: 1198

Pathways

Reactome:

RAB GEFs exchange GTP for GDP on RABs

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Hirschsprung disease, susceptibility to, 1	Likely pathogenic	rs1057519052	RCV000416370

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Acute myeloid leukemia	Benign	rs61732593	RCV005912077
Aganglionic megacolon	Uncertain significance	rs2289001, rs1045303	RCV000984710 RCV000984787
Clear cell carcinoma of kidney	Benign	rs61732593	RCV005912079
Nonpapillary renal cell carcinoma	Benign	rs61732593	RCV005912078
Ovarian serous cystadenocarcinoma	Benign	rs61732593	RCV005912080
Uterine corpus endometrial carcinoma	Benign	rs61732593	RCV005912081

Associations from Text Mining
Disease Name	Relationship Type	References
Carcinoma Basal Cell	Associate	36309102
Hemochromatosis	Associate	34583728
Iron Overload	Associate	34583728
Venous Thromboembolism	Associate	39848545