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	3631
Gene name	Inositol polyphosphate-4-phosphatase type I A
Gene symbol	INPP4A
Synonyms (NCBI Gene)	INPP4TVAS1
Chromosome	2
Chromosome location	2q11.2
Summary	This gene encodes an Mg++ independent enzyme that hydrolyzes the 4-position phosphate from the inositol ring of phosphatidylinositol 3,4-bisphosphate, inositol 1,3,4-trisphosphate, and inositol 3,4-bisphosphate. Multiple transcript variants encoding disti

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs1306444586	C>T	Likely-pathogenic	Non coding transcript variant, upstream transcript variant, synonymous variant, coding sequence variant, genic upstream transcript variant
rs1574887674	C>T	Pathogenic	Coding sequence variant, intron variant, non coding transcript variant, stop gained, genic upstream transcript variant, upstream transcript variant
rs1574965220	TC>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant

148

Show/Hide all (148)

miRTarBase ID	miRNA	Experiments	Reference
MIRT046283	hsa-miR-23b-3p	CLASH	23622248
MIRT039407	hsa-miR-421	CLASH	23622248
MIRT037226	hsa-miR-877-5p	CLASH	23622248
MIRT037226	hsa-miR-877-5p	CLASH	23622248
MIRT036040	hsa-miR-1301-3p	CLASH	23622248
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	20371350
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	20371350
MIRT522991	hsa-miR-525-5p	PAR-CLIP	20371350
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	20371350
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	20371350
MIRT522991	hsa-miR-525-5p	PAR-CLIP	20371350
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	23446348
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	23446348
MIRT522991	hsa-miR-525-5p	PAR-CLIP	23446348
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	20371350
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	20371350
MIRT522991	hsa-miR-525-5p	PAR-CLIP	20371350
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	20371350
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	20371350
MIRT522991	hsa-miR-525-5p	PAR-CLIP	20371350
MIRT522993	hsa-miR-3613-3p	PAR-CLIP	23446348
MIRT522992	hsa-miR-520a-5p	PAR-CLIP	23446348
MIRT522991	hsa-miR-525-5p	PAR-CLIP	23446348
MIRT1067111	hsa-miR-128	CLIP-seq
MIRT1067112	hsa-miR-200b	CLIP-seq
MIRT1067113	hsa-miR-200c	CLIP-seq
MIRT1067114	hsa-miR-223	CLIP-seq
MIRT1067115	hsa-miR-27a	CLIP-seq
MIRT1067116	hsa-miR-27b	CLIP-seq
MIRT1067117	hsa-miR-3123	CLIP-seq
MIRT1067118	hsa-miR-323-3p	CLIP-seq
MIRT1067119	hsa-miR-3919	CLIP-seq
MIRT1067120	hsa-miR-4255	CLIP-seq
MIRT1067121	hsa-miR-4276	CLIP-seq
MIRT1067122	hsa-miR-429	CLIP-seq
MIRT1067123	hsa-miR-4297	CLIP-seq
MIRT1067124	hsa-miR-4302	CLIP-seq
MIRT1067125	hsa-miR-4461	CLIP-seq
MIRT1067126	hsa-miR-4697-3p	CLIP-seq
MIRT1067127	hsa-miR-4724-5p	CLIP-seq
MIRT1067128	hsa-miR-4756-3p	CLIP-seq
MIRT1067129	hsa-miR-4777-3p	CLIP-seq
MIRT1067130	hsa-miR-4795-3p	CLIP-seq
MIRT1067131	hsa-miR-513a-5p	CLIP-seq
MIRT1067132	hsa-miR-532-5p	CLIP-seq
MIRT1067133	hsa-miR-592	CLIP-seq
MIRT1067134	hsa-miR-597	CLIP-seq
MIRT1067135	hsa-miR-616	CLIP-seq
MIRT1067136	hsa-miR-935	CLIP-seq
MIRT1067137	hsa-miR-1305	CLIP-seq
MIRT1067138	hsa-miR-188-5p	CLIP-seq
MIRT1067139	hsa-miR-204	CLIP-seq
MIRT1067140	hsa-miR-211	CLIP-seq
MIRT1067141	hsa-miR-30a	CLIP-seq
MIRT1067142	hsa-miR-30b	CLIP-seq
MIRT1067143	hsa-miR-30c	CLIP-seq
MIRT1067144	hsa-miR-30d	CLIP-seq
MIRT1067145	hsa-miR-30e	CLIP-seq
MIRT1067146	hsa-miR-3136-3p	CLIP-seq
MIRT1067147	hsa-miR-3944-5p	CLIP-seq
MIRT1067148	hsa-miR-4432	CLIP-seq
MIRT1067149	hsa-miR-4495	CLIP-seq
MIRT1067150	hsa-miR-455-5p	CLIP-seq
MIRT1067151	hsa-miR-4698	CLIP-seq
MIRT1067152	hsa-miR-498	CLIP-seq
MIRT1067153	hsa-miR-499-5p	CLIP-seq
MIRT1067154	hsa-miR-605	CLIP-seq
MIRT1067155	hsa-miR-607	CLIP-seq
MIRT1067156	hsa-miR-1323	CLIP-seq
MIRT1067157	hsa-miR-137	CLIP-seq
MIRT1067139	hsa-miR-204	CLIP-seq
MIRT1067140	hsa-miR-211	CLIP-seq
MIRT1067158	hsa-miR-25	CLIP-seq
MIRT1067159	hsa-miR-300	CLIP-seq
MIRT1067160	hsa-miR-32	CLIP-seq
MIRT1067161	hsa-miR-338-5p	CLIP-seq
MIRT1067162	hsa-miR-363	CLIP-seq
MIRT1067163	hsa-miR-367	CLIP-seq
MIRT1067164	hsa-miR-381	CLIP-seq
MIRT1067165	hsa-miR-3938	CLIP-seq
MIRT1067166	hsa-miR-4328	CLIP-seq
MIRT1067167	hsa-miR-4470	CLIP-seq
MIRT1067168	hsa-miR-4666-3p	CLIP-seq
MIRT1067169	hsa-miR-4742-3p	CLIP-seq
MIRT1067170	hsa-miR-4753-3p	CLIP-seq
MIRT1067171	hsa-miR-4755-5p	CLIP-seq
MIRT1067172	hsa-miR-4789-5p	CLIP-seq
MIRT1067173	hsa-miR-548a-3p	CLIP-seq
MIRT1067174	hsa-miR-548a-5p	CLIP-seq
MIRT1067175	hsa-miR-548ab	CLIP-seq
MIRT1067176	hsa-miR-548ak	CLIP-seq
MIRT1067177	hsa-miR-548b-5p	CLIP-seq
MIRT1067178	hsa-miR-548c-5p	CLIP-seq
MIRT1067179	hsa-miR-548d-5p	CLIP-seq
MIRT1067180	hsa-miR-548e	CLIP-seq
MIRT1067181	hsa-miR-548f	CLIP-seq
MIRT1067182	hsa-miR-548g	CLIP-seq
MIRT1067183	hsa-miR-548h	CLIP-seq
MIRT1067184	hsa-miR-548i	CLIP-seq
MIRT1067185	hsa-miR-548j	CLIP-seq
MIRT1067186	hsa-miR-548o	CLIP-seq
MIRT1067187	hsa-miR-548w	CLIP-seq
MIRT1067188	hsa-miR-548y	CLIP-seq
MIRT1067189	hsa-miR-559	CLIP-seq
MIRT1067190	hsa-miR-580	CLIP-seq
MIRT1067191	hsa-miR-587	CLIP-seq
MIRT1067192	hsa-miR-623	CLIP-seq
MIRT1067193	hsa-miR-802	CLIP-seq
MIRT1067194	hsa-miR-92a	CLIP-seq
MIRT1067195	hsa-miR-92b	CLIP-seq
MIRT1067196	hsa-miR-944	CLIP-seq
MIRT2016267	hsa-miR-1910	CLIP-seq
MIRT1067112	hsa-miR-200b	CLIP-seq
MIRT1067113	hsa-miR-200c	CLIP-seq
MIRT2016268	hsa-miR-4274	CLIP-seq
MIRT1067122	hsa-miR-429	CLIP-seq
MIRT2016269	hsa-miR-4744	CLIP-seq
MIRT1067112	hsa-miR-200b	CLIP-seq
MIRT1067113	hsa-miR-200c	CLIP-seq
MIRT1067122	hsa-miR-429	CLIP-seq
MIRT1067111	hsa-miR-128	CLIP-seq
MIRT2552050	hsa-miR-1304	CLIP-seq
MIRT2552051	hsa-miR-143	CLIP-seq
MIRT2552052	hsa-miR-15a	CLIP-seq
MIRT2552053	hsa-miR-15b	CLIP-seq
MIRT2552054	hsa-miR-16	CLIP-seq
MIRT2552055	hsa-miR-195	CLIP-seq
MIRT2552056	hsa-miR-3064-3p	CLIP-seq
MIRT2552057	hsa-miR-3117-5p	CLIP-seq
MIRT2552058	hsa-miR-3126-5p	CLIP-seq
MIRT2552059	hsa-miR-409-5p	CLIP-seq
MIRT2552060	hsa-miR-424	CLIP-seq
MIRT2552061	hsa-miR-4419a	CLIP-seq
MIRT2552062	hsa-miR-4428	CLIP-seq
MIRT2552063	hsa-miR-4510	CLIP-seq
MIRT2552064	hsa-miR-4530	CLIP-seq
MIRT2552065	hsa-miR-4680-5p	CLIP-seq
MIRT2552066	hsa-miR-4691-3p	CLIP-seq
MIRT1067128	hsa-miR-4756-3p	CLIP-seq
MIRT2552067	hsa-miR-4770	CLIP-seq
MIRT2552068	hsa-miR-497	CLIP-seq
MIRT2552069	hsa-miR-512-5p	CLIP-seq
MIRT2552070	hsa-miR-634	CLIP-seq
MIRT2552071	hsa-miR-640	CLIP-seq
MIRT2552072	hsa-miR-922	CLIP-seq
MIRT2682844	hsa-miR-1973	CLIP-seq
MIRT2682845	hsa-miR-3150a-5p	CLIP-seq
MIRT2682846	hsa-miR-3150b-5p	CLIP-seq

Show/Hide all (34)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25869668
GO:0005634	Component	Nucleus	IDA	30071275
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	30071275
GO:0005737	Component	Cytoplasm	IEA
GO:0005768	Component	Endosome	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005886	Component	Plasma membrane	IEA
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006661	Process	Phosphatidylinositol biosynthetic process	IEA
GO:0006661	Process	Phosphatidylinositol biosynthetic process	TAS
GO:0007165	Process	Signal transduction	TAS	7608176
GO:0014069	Component	Postsynaptic density	IEA
GO:0014069	Component	Postsynaptic density	ISS
GO:0016020	Component	Membrane	IEA
GO:0016316	Function	Phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity	IBA
GO:0016316	Function	Phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity	IEA
GO:0016316	Function	Phosphatidylinositol-3,4-bisphosphate 4-phosphatase activity	TAS
GO:0016787	Function	Hydrolase activity	IEA
GO:0016791	Function	Phosphatase activity	IEA
GO:0017161	Function	Inositol-1,3,4-trisphosphate 4-phosphatase activity	IEA
GO:0017161	Function	Inositol-1,3,4-trisphosphate 4-phosphatase activity	TAS
GO:0031901	Component	Early endosome membrane	IEA
GO:0031965	Component	Nuclear membrane	IDA
GO:0036092	Process	Phosphatidylinositol-3-phosphate biosynthetic process	IEA
GO:0043226	Component	Organelle	IEA
GO:0043647	Process	Inositol phosphate metabolic process	TAS
GO:0044281	Process	Small molecule metabolic process	IEA
GO:0045202	Component	Synapse	IEA
GO:0052828	Function	Inositol-3,4-bisphosphate 4-phosphatase activity	IEA
GO:0052828	Function	Inositol-3,4-bisphosphate 4-phosphatase activity	TAS
GO:0055038	Component	Recycling endosome membrane	IEA

MIM	HGNC	e!Ensembl
600916	6074	ENSG00000040933

Q96PE3

Protein name

Inositol polyphosphate-4-phosphatase type I A (Inositol polyphosphate 4-phosphatase type I) (Type I inositol 3,4-bisphosphate 4-phosphatase) (EC 3.1.3.66)

Protein function

Catalyzes the hydrolysis of the 4-position phosphate of phosphatidylinositol 3,4-bisphosphate (PtdIns(3,4)P2) (PubMed:15716355, PubMed:20463662). Also catalyzes inositol 1,3,4-trisphosphate and inositol 1,4-bisphosphate (By similarity). Antagoni

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Isoform 1 is expressed in the platelets, MEG-01 megakaryocytes and Jurkat T-cells. Isoform 2 is expressed in the brain. {ECO:0000269|PubMed:11485317}.

Sequence

MTAREHSPRHGARARAMQRASTIDVAADMLGLSLAGNIQDPDEPILEFSLACSELHTPSL
DRKPNSFVAVSVTTPPQAFWTKHAQTEIIEGTNNPIFLSSIAFFQDSLINQMTQVKLSVY
DVKDRSQGTMYLLGSGTFIVKDLLQDRHHRLHLTLRSAESDRVGNITVIGWQMEEKSDQR
PPVTRSVDTVNGRMVLPVDESLTEALGIRSKYASLRKDTLLKSVFGGAICRMYRFPTTDG
NHLRILEQMAESVLSLHVPRQFVKLLLEEDAARVCELEELGELSPCWESLRRQIVTQYQT
IILTYQENLTDLHQYRGPSFKASSLKADKKLEFVPTNLHIQRMRVQDDGGSDQNYDIVTI
GAPAAHCQGFKSGGLRKKLHKFEETKKHFEECCTSSGCQSIIYIPQDVVRAKEIIAQINT
LKTQVSYYAERLSRAAKDRSATGLERTLAILADKTRQLVTVCDCKLLANSIHGLNAARPD
YIASKASPTSTEEEQVMLRNDQDTLMARWTGRNSRSSLQVDWHEEEWEKVWLNVDKSLEC
IIQRVDKLLQKERLHGEGCEDVFPCAGSCTSKKGNPDSHAYWIRPEDPFCDVPSSPCPST
MPSTACHPHLTTHCSPPPEESSPGEWSEALYPLLTTLTDCVAMMSDKAKKAMVFLLMQDS
APTIATYLSLQYRRDVVFCQTLTALICGFIIKLRNCLHDDGFLRQLYTIGLLAQFESLLS
TYGEELAMLEDMSLGIMDLRNVTFKVTQATSSASADMLPVITGNRDGFNVRVPLPGPLFD
ALPREIQSGMLLRVQPVLFNVGINEQQTLAERFGDTSLQEVINVESLVRLNSYFEQFKEV
LPEDCLPRSRSQTCLPELLRFLGQNVHARKNKNVDILWQAAEICRRLNGVRFTSCKSAKD
RTAMSVTLEQCLILQHEHGMAPQVFTQALECMRSEGCRRENTMKNVGSRKYAFNSLQLKA
FPKHYRPPEGTYGKVET

Sequence length

977

Interactions

View interactions

	KEGG		Reactome
	Inositol phosphate metabolism Metabolic pathways Phosphatidylinositol signaling system		Synthesis of PIPs at the plasma membrane Synthesis of PIPs at the early endosome membrane Synthesis of IP2, IP, and Ins in the cytosol

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 (8)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Dyskeratosis congenita, autosomal dominant 1	Likely pathogenic	rs1306444586	RCV000761361	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hypotonia	Likely pathogenic	rs1574965220	RCV000991365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability	Pathogenic	rs1574887674	RCV000986112	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Microcephaly	Likely pathogenic	rs1574965220	RCV000991365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
NEURODEVELOPMENTAL DISORDER WITH GROWTH IMPAIRMENT, QUADRIPARESIS, AND POOR OR ABSENT SPEECH	Likely pathogenic; Pathogenic	rs1574965220, rs267599505	RCV005860165 RCV005860519	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nystagmus	Likely pathogenic	rs1574965220	RCV000991365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Pectus excavatum	Likely pathogenic	rs1574965220	RCV000991365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
visual disturbance	Likely pathogenic	rs1574965220	RCV000991365	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (5)

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.
BIPOLAR DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CARCINOMA, BASAL CELL	—	CTD	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MENTAL RETARDATION	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEURODEVELOPMENTAL DISORDERS	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (22)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
Asthma	Asthma	BEFREE	18187694, 30335467		★★★★★ ★☆☆☆☆ Found in Text Mining only
Asthma	Asthma	LHGDN	18187694		★★★★★ ★☆☆☆☆ Found in Text Mining only
Bladder Neoplasm	Bladder Neoplasm	BEFREE	28337959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma of bladder	Bladder carcinoma	BEFREE	28337959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Pancreatic Ductal	Pancreatic ductal carcinoma	Pubtator	35856354	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	29415082	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	30809968	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus Type 1	Diabetes mellitus, type 1	Pubtator	34006268	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
DYSKERATOSIS CONGENITA, AUTOSOMAL DOMINANT 1	Dyskeratosis Congenita	CLINVAR_DG	15849264, 21931702		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Esophageal carcinoma	Esophageal Carcinoma	BEFREE	29880087		★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	CTD_human_DG	21937992		★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Malignant neoplasm of pancreas	Pancreatic cancer	BEFREE	27733216		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of urinary bladder	Urinary bladder cancer	BEFREE	28337959		★★★★★ ★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	28337959, 30809968, 31831620		★★★★★ ★☆☆☆☆ Found in Text Mining only
Mental deficiency	Mental retardation	CTD_human_DG	21937992		★★★★★ ★☆☆☆☆ Found in Text Mining only
Myoclonic Epilepsy	Myoclonic Epilepsy	BEFREE	25338135		★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	28776573		★★★★★ ★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	30001772		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	27733216		★★★★★ ★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasms	Pancreatic neoplasm	Pubtator	27733216, 29415082	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Profound Mental Retardation	Mental retardation	CTD_human_DG	21937992		★★★★★ ★☆☆☆☆ Found in Text Mining only
Urinary Bladder Neoplasms	Urinary bladder neoplasms	Pubtator	28337959	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only

INPP4A (inositol polyphosphate-4-phosphatase type I A)