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	23258
Gene name	DENN domain containing 5A
Gene symbol	DENND5A
Synonyms (NCBI Gene)	DEE49EIEE49RAB6IP1
Chromosome	11
Chromosome location	11p15.4
Summary	This gene encodes a DENN-domain-containing protein that functions as a RAB-activating guanine nucleotide exchange factor (GEF). This protein catalyzes the conversion of GDP to GTP and thereby converts inactive GDP-bound Rab proteins into their active GTP-

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1057519307	CT>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1057519308	C>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1057519310	G>-	Pathogenic	Non coding transcript variant, 3 prime UTR variant, coding sequence variant, frameshift variant
rs1057519563	G>A	Likely-pathogenic	Non coding transcript variant, stop gained, coding sequence variant
rs1057519564	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1590275695	AC>-	Likely-pathogenic	5 prime UTR variant, coding sequence variant, frameshift variant, non coding transcript variant

174

Show/Hide all (174)

miRTarBase ID	miRNA	Experiments	Reference
MIRT050288	hsa-miR-25-3p	CLASH	23622248
MIRT049154	hsa-miR-92a-3p	CLASH	23622248
MIRT047785	hsa-miR-30d-5p	CLASH	23622248
MIRT932596	hsa-miR-1183	CLIP-seq
MIRT932597	hsa-miR-1250	CLIP-seq
MIRT932598	hsa-miR-188-5p	CLIP-seq
MIRT932599	hsa-miR-204	CLIP-seq
MIRT932600	hsa-miR-211	CLIP-seq
MIRT932601	hsa-miR-3137	CLIP-seq
MIRT932602	hsa-miR-4327	CLIP-seq
MIRT932603	hsa-miR-4477a	CLIP-seq
MIRT932604	hsa-miR-4640-5p	CLIP-seq
MIRT932605	hsa-miR-4668-3p	CLIP-seq
MIRT932606	hsa-miR-4726-5p	CLIP-seq
MIRT932607	hsa-miR-545	CLIP-seq
MIRT932608	hsa-miR-548c-3p	CLIP-seq
MIRT932609	hsa-miR-605	CLIP-seq
MIRT932610	hsa-miR-618	CLIP-seq
MIRT932611	hsa-miR-636	CLIP-seq
MIRT932612	hsa-miR-877	CLIP-seq
MIRT1976134	hsa-miR-1227	CLIP-seq
MIRT1976135	hsa-miR-2053	CLIP-seq
MIRT1976136	hsa-miR-409-3p	CLIP-seq
MIRT1976137	hsa-miR-4261	CLIP-seq
MIRT1976138	hsa-miR-4449	CLIP-seq
MIRT1976139	hsa-miR-4496	CLIP-seq
MIRT1976140	hsa-miR-4536	CLIP-seq
MIRT1976141	hsa-miR-4738-3p	CLIP-seq
MIRT1976142	hsa-miR-4803	CLIP-seq
MIRT1976143	hsa-miR-494	CLIP-seq
MIRT1976144	hsa-miR-548g	CLIP-seq
MIRT1976145	hsa-miR-569	CLIP-seq
MIRT1976146	hsa-miR-889	CLIP-seq
MIRT932596	hsa-miR-1183	CLIP-seq
MIRT1976134	hsa-miR-1227	CLIP-seq
MIRT2211528	hsa-miR-1271	CLIP-seq
MIRT2211529	hsa-miR-182	CLIP-seq
MIRT2211530	hsa-miR-200b	CLIP-seq
MIRT2211531	hsa-miR-200c	CLIP-seq
MIRT2211532	hsa-miR-2114	CLIP-seq
MIRT2211533	hsa-miR-23a	CLIP-seq
MIRT2211534	hsa-miR-23b	CLIP-seq
MIRT2211535	hsa-miR-23c	CLIP-seq
MIRT932601	hsa-miR-3137	CLIP-seq
MIRT2211536	hsa-miR-3174	CLIP-seq
MIRT2211537	hsa-miR-3182	CLIP-seq
MIRT2211538	hsa-miR-34c-3p	CLIP-seq
MIRT2211539	hsa-miR-3667-3p	CLIP-seq
MIRT2211540	hsa-miR-3682-5p	CLIP-seq
MIRT2211541	hsa-miR-425	CLIP-seq
MIRT2211542	hsa-miR-429	CLIP-seq
MIRT2211543	hsa-miR-4304	CLIP-seq
MIRT2211544	hsa-miR-4307	CLIP-seq
MIRT932603	hsa-miR-4477a	CLIP-seq
MIRT1976140	hsa-miR-4536	CLIP-seq
MIRT2211545	hsa-miR-4639-3p	CLIP-seq
MIRT932604	hsa-miR-4640-5p	CLIP-seq
MIRT2211546	hsa-miR-4677-3p	CLIP-seq
MIRT2211547	hsa-miR-4679	CLIP-seq
MIRT2211548	hsa-miR-4717-3p	CLIP-seq
MIRT2211549	hsa-miR-4720-3p	CLIP-seq
MIRT932606	hsa-miR-4726-5p	CLIP-seq
MIRT1976141	hsa-miR-4738-3p	CLIP-seq
MIRT1976144	hsa-miR-548g	CLIP-seq
MIRT2211550	hsa-miR-564	CLIP-seq
MIRT2211551	hsa-miR-642b	CLIP-seq
MIRT2211552	hsa-miR-96	CLIP-seq
MIRT2211530	hsa-miR-200b	CLIP-seq
MIRT2211531	hsa-miR-200c	CLIP-seq
MIRT2211539	hsa-miR-3667-3p	CLIP-seq
MIRT2211542	hsa-miR-429	CLIP-seq
MIRT2211543	hsa-miR-4304	CLIP-seq
MIRT2211551	hsa-miR-642b	CLIP-seq
MIRT2515234	hsa-miR-1228	CLIP-seq
MIRT932597	hsa-miR-1250	CLIP-seq
MIRT2515235	hsa-miR-1321	CLIP-seq
MIRT2515236	hsa-miR-147	CLIP-seq
MIRT2515237	hsa-miR-1471	CLIP-seq
MIRT932598	hsa-miR-188-5p	CLIP-seq
MIRT2515238	hsa-miR-1910	CLIP-seq
MIRT932599	hsa-miR-204	CLIP-seq
MIRT1976135	hsa-miR-2053	CLIP-seq
MIRT932600	hsa-miR-211	CLIP-seq
MIRT2515239	hsa-miR-2115	CLIP-seq
MIRT2515240	hsa-miR-24	CLIP-seq
MIRT2515241	hsa-miR-3064-3p	CLIP-seq
MIRT2515242	hsa-miR-3155	CLIP-seq
MIRT2515243	hsa-miR-3155b	CLIP-seq
MIRT2515244	hsa-miR-3199	CLIP-seq
MIRT2515245	hsa-miR-338-3p	CLIP-seq
MIRT2515246	hsa-miR-3613-3p	CLIP-seq
MIRT2515247	hsa-miR-3662	CLIP-seq
MIRT2211539	hsa-miR-3667-3p	CLIP-seq
MIRT2515248	hsa-miR-3675-5p	CLIP-seq
MIRT2515249	hsa-miR-3911	CLIP-seq
MIRT1976136	hsa-miR-409-3p	CLIP-seq
MIRT2515250	hsa-miR-4264	CLIP-seq
MIRT2515251	hsa-miR-4270	CLIP-seq
MIRT2515252	hsa-miR-4283	CLIP-seq
MIRT2515253	hsa-miR-4285	CLIP-seq
MIRT2211543	hsa-miR-4304	CLIP-seq
MIRT932602	hsa-miR-4327	CLIP-seq
MIRT2515254	hsa-miR-4419a	CLIP-seq
MIRT2515255	hsa-miR-4438	CLIP-seq
MIRT2515256	hsa-miR-4441	CLIP-seq
MIRT2515257	hsa-miR-4489	CLIP-seq
MIRT2515258	hsa-miR-4510	CLIP-seq
MIRT2515259	hsa-miR-4530	CLIP-seq
MIRT2515260	hsa-miR-455-3p	CLIP-seq
MIRT2515261	hsa-miR-4648	CLIP-seq
MIRT932605	hsa-miR-4668-3p	CLIP-seq
MIRT2515262	hsa-miR-4685-5p	CLIP-seq
MIRT2515263	hsa-miR-4701-5p	CLIP-seq
MIRT2515264	hsa-miR-4728-5p	CLIP-seq
MIRT2515265	hsa-miR-4739	CLIP-seq
MIRT2515266	hsa-miR-4740-5p	CLIP-seq
MIRT2515267	hsa-miR-4756-5p	CLIP-seq
MIRT2515268	hsa-miR-484	CLIP-seq
MIRT2515269	hsa-miR-509-3p	CLIP-seq
MIRT932608	hsa-miR-548c-3p	CLIP-seq
MIRT1976145	hsa-miR-569	CLIP-seq
MIRT2515270	hsa-miR-588	CLIP-seq
MIRT932609	hsa-miR-605	CLIP-seq
MIRT932611	hsa-miR-636	CLIP-seq
MIRT2211551	hsa-miR-642b	CLIP-seq
MIRT2515271	hsa-miR-644	CLIP-seq
MIRT2515272	hsa-miR-663b	CLIP-seq
MIRT932612	hsa-miR-877	CLIP-seq
MIRT1976146	hsa-miR-889	CLIP-seq
MIRT2515234	hsa-miR-1228	CLIP-seq
MIRT932597	hsa-miR-1250	CLIP-seq
MIRT2515235	hsa-miR-1321	CLIP-seq
MIRT2515236	hsa-miR-147	CLIP-seq
MIRT2515237	hsa-miR-1471	CLIP-seq
MIRT932598	hsa-miR-188-5p	CLIP-seq
MIRT2515238	hsa-miR-1910	CLIP-seq
MIRT2211530	hsa-miR-200b	CLIP-seq
MIRT2211531	hsa-miR-200c	CLIP-seq
MIRT932599	hsa-miR-204	CLIP-seq
MIRT1976135	hsa-miR-2053	CLIP-seq
MIRT932600	hsa-miR-211	CLIP-seq
MIRT2515240	hsa-miR-24	CLIP-seq
MIRT2515241	hsa-miR-3064-3p	CLIP-seq
MIRT2515242	hsa-miR-3155	CLIP-seq
MIRT2515243	hsa-miR-3155b	CLIP-seq
MIRT2211539	hsa-miR-3667-3p	CLIP-seq
MIRT2515248	hsa-miR-3675-5p	CLIP-seq
MIRT2515249	hsa-miR-3911	CLIP-seq
MIRT1976136	hsa-miR-409-3p	CLIP-seq
MIRT2515250	hsa-miR-4264	CLIP-seq
MIRT2515251	hsa-miR-4270	CLIP-seq
MIRT2515252	hsa-miR-4283	CLIP-seq
MIRT2211542	hsa-miR-429	CLIP-seq
MIRT2211543	hsa-miR-4304	CLIP-seq
MIRT932602	hsa-miR-4327	CLIP-seq
MIRT2515255	hsa-miR-4438	CLIP-seq
MIRT2515256	hsa-miR-4441	CLIP-seq
MIRT2515257	hsa-miR-4489	CLIP-seq
MIRT2515260	hsa-miR-455-3p	CLIP-seq
MIRT932605	hsa-miR-4668-3p	CLIP-seq
MIRT2515262	hsa-miR-4685-5p	CLIP-seq
MIRT2515265	hsa-miR-4739	CLIP-seq
MIRT2515267	hsa-miR-4756-5p	CLIP-seq
MIRT2515268	hsa-miR-484	CLIP-seq
MIRT2515269	hsa-miR-509-3p	CLIP-seq
MIRT932608	hsa-miR-548c-3p	CLIP-seq
MIRT1976145	hsa-miR-569	CLIP-seq
MIRT932609	hsa-miR-605	CLIP-seq
MIRT932611	hsa-miR-636	CLIP-seq
MIRT2211551	hsa-miR-642b	CLIP-seq
MIRT2515271	hsa-miR-644	CLIP-seq
MIRT2515272	hsa-miR-663b	CLIP-seq
MIRT932612	hsa-miR-877	CLIP-seq
MIRT1976146	hsa-miR-889	CLIP-seq

Show/Hide all (18)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0005085	Function	Guanyl-nucleotide exchange factor activity	IBA
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:0005515	Function	Protein binding	IPI	32296183
GO:0005794	Component	Golgi apparatus	IEA
GO:0005802	Component	Trans-Golgi network	IBA
GO:0005802	Component	Trans-Golgi network	IDA	19619496
GO:0005829	Component	Cytosol	TAS
GO:0010977	Process	Negative regulation of neuron projection development	IEA
GO:0010977	Process	Negative regulation of neuron projection development	ISS
GO:0016020	Component	Membrane	IEA
GO:0030904	Component	Retromer complex	IDA	19619496
GO:0031267	Function	Small GTPase binding	IBA
GO:0031267	Function	Small GTPase binding	IEA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IBA
GO:0042147	Process	Retrograde transport, endosome to Golgi	IMP	19619496

MIM	HGNC	e!Ensembl
617278	19344	ENSG00000184014

Q6IQ26

Protein name

DENN domain-containing protein 5A (Rab6-interacting protein 1) (Rab6IP1)

Protein function

Guanine nucleotide exchange factor (GEF) which may activate RAB6A and RAB39A and/or RAB39B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. Involved in the negative regulation of

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03456	uDENN	75 → 137	uDENN domain	Domain
PF02141	DENN	202 → 390	DENN (AEX-3) domain	Family
PF03455	dDENN	555 → 607	dDENN domain	Domain
PF02759	RUN	795 → 947	RUN domain	Family
PF01477	PLAT	956 → 1062	PLAT/LH2 domain	Domain
PF02759	RUN	1142 → 1281	RUN domain	Family

Sequence

MSGGGGGGGSAPSRFADYFVICGLDTETGLEPDELSALCQYIQASKARDGASPFISSTTE
GENFEQTPLRRTFKSKVLARYPENVEWNPFDQDAVGMLCMPKGLAFKTQADPREPQFHAF
IITREDGSRTFGFALTFYEEVTSKQICSAMQTLYHMHNAEYDVLHAPPADDRDQSSMEDG
EDTPVTKLQRFNSYDISRDTLYVSKCICLITPMSFMKACRSVLEQLHQAVTSPQPPPLPL
ESYIYNVLYEVPLPPPGRSLKFSGVYGPIICQRPSTNELPLFDFPVKEVFELLGVENVFQ
LFTCALLEFQILLYSQHYQRLMTVAETITALMFPFQWQHVYVPILPASLLHFLDAPVPYL
MGLHSNGLDDRSKLELPQEANLCFVDIDNHFIELPEDLPQFPNKLEFVQEVSEILMAFGI
PPEGNLHCSESASKLKRLRASELVSDKRNGNIAGSPLHSYELLKENETIARLQALVKRTG
VSLEKLEVREDPSSNKDLKVQCDEEELRIYQLNIQIREVFANRFTQMFADYEVFVIQPSQ
DKESWFTNREQMQNFDKASFLSDQPEPYLPFLSRFLETQMFASFIDNKIMCHDDDDKDPV
LRVFDSRVDKIRLLNVRTPTLRTSMYQKCTTVDEAEKAIELRLAKIDHTAIHPHLLDMKI
GQGKYEPGFFPKLQSDVLSTGPASNKWTKRNAPAQWRRKDRQKQHTEHLRLDNDQREKYI
QEARTMGSTIRQPKLSNLSPSVIAQTNWKFVEGLLKECRNKTKRMLVEKMGREAVELGHG
EVNITGVEENTLIASLCDLLERIWSHGLQVKQGKSALWSHLLHYQDNRQRKLTSGSLSTS
GILLDSERRKSDASSLMPPLRISLIQDMRHIQNIGEIKTDVGKARAWVRLSMEKKLLSRH
LKQLLSDHELTKKLYKRYAFLRCDDEKEQFLYHLLSFNAVDYFCFTNVFTTILIPYHILI
VPSKKLGGSMFTANPWICISGELGETQIMQIPRNVLEMTFECQNLGKLTTVQIGHDNSGL
YAKWLVEYVMVRNEITGHTYKFPCGRWLGKGMDDGSLERILVGELLTSQPEVDERPCRTP
PLQQSPSVIRRLVTISPNNKPKLNTGQIQESIGEAVNGIVKHFHKPEKERGSLTLLLCGE
CGLVSALEQAFQHGFKSPRLFKNVFIWDFLEKAQTYYETLEKNEVVPEENWHTRARNFCR
FVTAINNTPRNIGKDGKFQMLVCLGARDHLLHHWIALLADCPITAHMYEDVALIKDHTLV
NSLIRVLQTLQEFNITLETSLVKGIDI

Sequence length

1287

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 (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
DENND5A-related disorder	Likely pathogenic; Pathogenic	rs1378771732, rs1057519563	RCV003983334 RCV003950331	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental and epileptic encephalopathy, 49	Likely pathogenic; Pathogenic	rs1849592470, rs1381160481, rs2493741184, rs1057519307, rs1057519308, rs1057519310, rs1057519563, rs1057519564	RCV001808304 RCV003322692 RCV003493229 RCV000415577 RCV000415606 RCV000415582 RCV000416961 RCV000416977 View all (3 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Show/Hide Unknown Diseases (16)

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
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CORONARY ARTERY DISEASE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY 49	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GILLES DE LA TOURETTE SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR HYPERTENSION	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ 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 (10)

Disease Name	Disease (Merged)	Source	PMID	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Epileptic encephalopathy	Epileptic encephalopathy	GENOMICS_ENGLAND_DG	27431290, 27866705	★★★★★ ★☆☆☆☆ Found in Text Mining only
Epileptic encephalopathy	Epileptic encephalopathy	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 49	Epileptic encephalopathy	GENOMICS_ENGLAND_DG	27431290	★★★★★ ★☆☆☆☆ Found in Text Mining only
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 49	Epileptic encephalopathy	UNIPROT_DG	27431290, 27866705	★★★★★ ★☆☆☆☆ Found in Text Mining only
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 49	Epileptic encephalopathy	CLINVAR_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
EPILEPTIC ENCEPHALOPATHY, EARLY INFANTILE, 49	Epileptic encephalopathy	CTD_human_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Frontal bossing	Frontal bossing	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only
Profound global developmental delay	Developmental Delay	HPO_DG		★★★★★ ★☆☆☆☆ Found in Text Mining only

DENND5A (DENN domain containing 5A)