ARAP3 (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3)

Gene

• Entrez ID: 64411
• Gene name: ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3
• Gene symbol: ARAP3
• Synonyms (NCBI Gene): CENTD3, DRAG1
• Chromosome: 5
• Chromosome location: 5q31.3
• Summary: This gene encodes a phosphoinositide binding protein containing ARF-GAP, RHO-GAP, RAS-associating, and pleckstrin homology domains. The ARF-GAP and RHO-GAP domains cooperate in mediating rearrangements in the cell cytoskeleton and cell shape. It is a spec

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT791715	hsa-miR-135a	CLIP-seq
MIRT791716	hsa-miR-135b	CLIP-seq
MIRT791717	hsa-miR-3143	CLIP-seq
MIRT791718	hsa-miR-499-3p	CLIP-seq
MIRT791719	hsa-miR-499a-3p	CLIP-seq
MIRT791720	hsa-miR-760	CLIP-seq
MIRT1933596	hsa-miR-142-5p	CLIP-seq
MIRT1933597	hsa-miR-340	CLIP-seq
MIRT1933598	hsa-miR-3671	CLIP-seq
MIRT1933599	hsa-miR-410	CLIP-seq
MIRT2173665	hsa-miR-548aa	CLIP-seq
MIRT2173665	hsa-miR-548aa	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001726	Component	Ruffle	IEA
GO:0005096	Function	GTPase activator activity	ISS
GO:0005515	Function	Protein binding	IPI	15090612, 31980649
GO:0005547	Function	Phosphatidylinositol-3,4,5-trisphosphate binding	IBA
GO:0005547	Function	Phosphatidylinositol-3,4,5-trisphosphate binding	IDA	11804589
GO:0005547	Function	Phosphatidylinositol-3,4,5-trisphosphate binding	IEA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0007010	Process	Cytoskeleton organization	TAS	15569923
GO:0007165	Process	Signal transduction	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	TAS	15569923
GO:0030027	Component	Lamellipodium	IEA
GO:0032956	Process	Regulation of actin cytoskeleton organization	IBA
GO:0042995	Component	Cell projection	IEA
GO:0043325	Function	Phosphatidylinositol-3,4-bisphosphate binding	IDA	11804589
GO:0046872	Function	Metal ion binding	IEA

Other IDs

• MIM: 606647
• HGNC: 24097
• e!Ensembl: ENSG00000120318

Protein

• UniProt ID: Q8WWN8
• Protein name: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 (Centaurin-delta-3) (Cnt-d3)
• Protein function: Phosphatidylinositol 3,4,5-trisphosphate-dependent GTPase-activating protein that modulates actin cytoskeleton remodeling by regulating ARF and RHO family members. Is activated by phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3) bindin
• PDB: 2KG5, 2LNW, 5JCP, 5JD0, 7A9B, 7YIR, 7YIS
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF07647	SAM_2	5 → 64	SAM domain (Sterile alpha motif)	Domain
  PF00169	PH	288 → 379	PH domain	Domain
  PF01412	ArfGap	489 → 607	Putative GTPase activating protein for Arf	Domain
  PF00620	RhoGAP	920 → 1073	RhoGAP domain	Domain
  PF00788	RA	1117 → 1210	Ras association (RalGDS/AF-6) domain	Domain
  PF00169	PH	1220 → 1325	PH domain	Domain

• Sequence:

  MAAPQDLDIAVWLATVHLEQYADTFRRHGLATAGAARGLGHEELKQLGISATGHRKRILR
  LLQTGTEEGSLDPKSDSAMEPSPSPAPQAQPPKPVPKPRTVFGGLSGPATTQRPGLSPAL
  GGPGVSRSPEPSPRPPPLPTSSSEQSSALNTVEMMPNSIYFGLDSRGRAQAAQDKAPDSS
  QISAPTPALRPTTGTVHIMDPGCLYYGVQPVGTPGAPDRRESRGVCQGRAEHRLSRQDLE
  AREDAGYASLELPGDSTLLSPTLETEETSDDLISPYASFSFTADRLTPLLSGWLDKLSPQ
  GNYVFQRRFVQFNGRSLMYFGSDKDPFPKGVIPLTAIEMTRSSKDNKFQVITGQRVFVFR
  TESEAQRDMWCSTLQSCLKEQRLLGHPRPPQPPRPLRTGMLELRGHKAKVFAALSPGELA
  LYKSEQAFSLGIGICFIELQGCSVRETKSRSFDLLTPHRCFSFTAESGGARQSWAAALQE
  AVTETLSDYEVAEKIWSNRANRQCADCGSSRPDWAAVNLGVVICKQCAGQHRALGSGISK
  VQSLKLDTSVWSNEIVQLFIVLGNDRANRFWAGTLPPGEGLHPDATPGPRGEFISRKYRL
  GLFRKPHPQYPDHSQLLQALCAAVARPNLLKNMTQLLCVEAFEGEEPWFPPAPDGSCPGL
  LPSDPSPGVYNEVVVRATYSGFLYCSPVSNKAGPSPPRRGRDAPPRLWCVLGAALEMFAS
  ENSPEPLSLIQPQDIVCLGVSPPPTDPGDRFPFSFELILAGGRIQHFGTDGADSLEAWTS
  AVGKWFSPLSCHQLLGPGLLRLGRLWLRSPSHTAPAPGLWLSGFGLLRGDHLFLCSAPGP
  GPPAPEDMVHLRRLQEISVVSAADTPDKKEHLVLVETGRTLYLQGEGRLDFTAWNAAIGG
  AAGGGGTGLQEQQMSRGDIPIIVDACISFVTQHGLRLEGVYRKGGARARSLRLLAEFRRD
  ARSVKLRPGEHFVEDVTDTLKRFFRELDDPVTSARLLPRWREAAELPQKNQRLEKYKDVI
  GCLPRVNRRTLATLIGHLYRVQKCAALNQMCTRNLALLFAPSVFQTDGRGEHEVRVLQEL
  IDGYISVFDIDSDQVAQIDLEVSLITTWKDVQLSQAGDLIMEVYIEQQLPDNCVTLKVSP
  TLTAEELTNQVLEMRGTAAGMDLWVTFEIREHGELERPLHPKEKVLEQALQWCQLPEPCS
  ASLLLKKVPLAQAGCLFTGIRRESPRVGLLRCREEPPRLLGSRFQERFFLLRGRCLLLLK
  EKKSSKPEREWPLEGAKVYLGIRKKLKPPTPWGFTLILEKMHLYLSCTDEDEMWDWTTSI
  LKAQHDDQQPVVLRRHSSSDLARQKFGTMPLLPIRGDDSGATLLSANQTLRRLHNRRTLS
  MFFPMKSSQGSVEEQEELEEPVYEEPVYEEVGAFPELIQDTSTSFSTTREWTVKPENPLT
  SQKSLDQPFLSKSSTLGQEERPPEPPPGPPSKSSPQARGSLEEQLLQELSSLILRKGETT
  AGLGSPSQPSSPQSPSPTGLPTQTPGFPTQPPCTSSPPSSQPLT

• Sequence length: 1544

Pathways

KEGG:

Rap1 signaling pathway
cAMP signaling pathway
Endocytosis

Reactome:

Rho GTPase cycle

Associated diseases

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
COLOR VISION DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
DIFFUSE LARGE B-CELL LYMPHOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INSOMNIA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG ADENOCARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CANCER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LUNG CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
METABOLIC SYNDROME	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
OCULAR HYPOTENSION	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PELVIC ORGAN PROLAPSE	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSYCHIATRIC DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SQUAMOUS CELL CARCINOMA	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Alzheimer Disease	Alzheimer disease	Pubtator	28800327	Associate	★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	Pubtator	28154144	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	28617548		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	25546409, 28617548	Associate	★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	17243165		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	17243165		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Diffuse Large B-Cell Lymphoma	Diffuse Lymphoma	GWASCAT_DG	25261932		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Inflammatory Bowel Diseases	Inflammatory bowel disease	Pubtator	28154144	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	25546409, 28617548		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	21076469		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	17243165		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	BEFREE	28617548		★☆☆☆☆ Found in Text Mining only
Moyamoya Disease	Moyamoya disease	Pubtator	40722175	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	25546409		★☆☆☆☆ Found in Text Mining only