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

Show/Hide all (1)

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

Show/Hide all (45)

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

Show/Hide all (9)

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

MIM	HGNC	e!Ensembl
617503	29134	ENSG00000105339

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

Interactions

View interactions

	Reactome
			RAB GEFs exchange GTP for GDP on RABs

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 (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Hirschsprung disease, susceptibility to, 1	Likely pathogenic	rs1057519052	RCV000416370	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (14)

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.
Acute myeloid leukemia	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Aganglionic megacolon	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CROHN'S DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HIRSCHSPRUNG DISEASE	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INFLAMMATORY BOWEL DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTESTINAL INFECTIOUS DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OBESITY	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TREATMENT-RESISTANT HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (5)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Carcinoma Basal Cell	Basal cell carcinoma	Pubtator	36309102	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Hemochromatosis	Hemochromatosis	Pubtator	34583728	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Iron Overload	Iron overload	Pubtator	34583728	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Narcolepsy	Narcolepsy	GWASDB_DG	19629137		★★★★★ ★☆☆☆☆ Found in Text Mining only
Venous Thromboembolism	Venous thromboembolism	Pubtator	39848545	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

DENND3 (DENN domain containing 3)