Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	11152
Gene name Gene Name - the full gene name approved by the HGNC.	WD repeat domain 45
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	WDR45
Synonyms (NCBI Gene) Gene synonyms aliases	JM5, NBIA4, NBIA5, WDRX1, WIPI-4, WIPI4
Chromosome Chromosome number	X
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	Xp11.23
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein com

Show/Hide all(26)

SNP ID	Visualize variation	Clinical significance	Consequence
rs201177026	C>G,T	Likely-pathogenic	Missense variant, coding sequence variant
rs387907331	->T	Pathogenic	Frameshift variant, coding sequence variant
rs797046101	G>A	Pathogenic-likely-pathogenic, pathogenic	Stop gained, coding sequence variant
rs864309661	CCA>-	Uncertain-significance, likely-pathogenic	Inframe deletion, coding sequence variant
rs886041382	G>A	Pathogenic	Stop gained, coding sequence variant
rs1057519622	AC>-	Pathogenic	Splice donor variant, intron variant
rs1057521933	C>T	Likely-pathogenic	Intron variant
rs1064794744	A>G	Likely-pathogenic	Missense variant, coding sequence variant
rs1557084239	->A	Pathogenic	Stop gained, coding sequence variant
rs1557084310	T>A	Pathogenic	Stop gained, coding sequence variant
rs1557084491	T>C	Likely-pathogenic	Splice acceptor variant
rs1557084549	G>A	Pathogenic	Stop gained, coding sequence variant
rs1569523502	TCAAAC>-	Likely-pathogenic	Coding sequence variant, inframe deletion
rs1569523537	->ACTA	Pathogenic	Coding sequence variant, stop gained
rs1569523544	CCTGCTCGTGGTCTGGACAGGGACCA>-	Pathogenic	Coding sequence variant, splice acceptor variant, intron variant
rs1569523562	G>A	Pathogenic	Coding sequence variant, stop gained
rs1569523565	A>T	Likely-pathogenic	Initiator codon variant, missense variant
rs1602539140	T>G	Pathogenic	Splice acceptor variant
rs1602539322	T>G	Likely-pathogenic	Intron variant
rs1602540060	G>C	Likely-pathogenic	Intron variant
rs1602540211	A>C	Pathogenic	Splice donor variant
rs1602540235	->T	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1602540295	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1602540331	A>G	Likely-pathogenic	Coding sequence variant, missense variant
rs1602540581	TGGCGCA>-	Pathogenic	Coding sequence variant, frameshift variant
rs1602540595	T>C	Likely-pathogenic	Splice acceptor variant

Show/Hide all(7)

miRTarBase ID	miRNA	Experiments	Reference
MIRT025809	hsa-miR-7-5p	Microarray	19073608
MIRT1490696	hsa-miR-1343	CLIP-seq
MIRT1490697	hsa-miR-193a-5p	CLIP-seq
MIRT1490698	hsa-miR-3667-3p	CLIP-seq
MIRT1490699	hsa-miR-3936	CLIP-seq
MIRT1490700	hsa-miR-4297	CLIP-seq
MIRT1490701	hsa-miR-639	CLIP-seq

Show/Hide all(23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000045	Process	Autophagosome assembly	IMP	28561066
GO:0000407	Component	Phagophore assembly site	IDA	28561066
GO:0000407	Component	Phagophore assembly site	IEA
GO:0000422	Process	Autophagy of mitochondrion	IBA
GO:0000425	Process	Pexophagy	IBA
GO:0005515	Function	Protein binding	IPI	20562859, 28561066, 31412244, 33961781, 34524948, 35271311
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0006914	Process	Autophagy	IEA
GO:0006914	Process	Autophagy	IMP	23435086
GO:0008289	Function	Lipid binding	IEA
GO:0009267	Process	Cellular response to starvation	IDA	28561066
GO:0019901	Function	Protein kinase binding	IPI	28561066
GO:0030674	Function	Protein-macromolecule adaptor activity	IBA
GO:0032266	Function	Phosphatidylinositol-3-phosphate binding	IBA
GO:0032266	Function	Phosphatidylinositol-3-phosphate binding	IDA	31271352
GO:0034045	Component	Phagophore assembly site membrane	IBA
GO:0034497	Process	Protein localization to phagophore assembly site	IBA
GO:0044804	Process	Nucleophagy	IBA
GO:0061723	Process	Glycophagy	IBA
GO:0080025	Function	Phosphatidylinositol-3,5-bisphosphate binding	IBA
GO:1901981	Function	Phosphatidylinositol phosphate binding	IDA	28561066
GO:2000786	Process	Positive regulation of autophagosome assembly	IDA	31271352

MIM	HGNC	e!Ensembl
300526	28912	ENSG00000196998

Protein

UniProt ID

Q9Y484

Protein name

WD repeat domain phosphoinositide-interacting protein 4 (WIPI-4) (WD repeat-containing protein 45)

Protein function

Component of the autophagy machinery that controls the major intracellular degradation process by which cytoplasmic materials are packaged into autophagosomes and delivered to lysosomes for degradation (PubMed:23435086, PubMed:28561066). Binds p

PDB

8KBX , 8KC3 , 8Y1L

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00400	WD40	226 → 264	WD domain, G-beta repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Ubiquitously expressed, with high expression in skeletal muscle and heart. Weakly expressed in liver and placenta. Expression is down-regulated in pancreatic and in kidney tumors. {ECO:0000269|PubMed:15602573}.

Sequence

MTQQPLRGVTSLRFNQDQSCFCCAMETGVRIYNVEPLMEKGHLDHEQVGSMGLVEMLHRS
NLLALVGGGSSPKFSEISVLIWDDAREGKDSKEKLVLEFTFTKPVLSVRMRHDKIVIVLK
NRIYVYSFPDNPRKLFEFDTRDNPKGLCDLCPSLEKQLLVFPGHKCGSLQLVDLASTKPG
TSSAPFTINAHQSDIACVSLNQPGTVVASASQKGTLIRLFDTQSKEKLVELRRGTDPATL
YCINFSHDSSFLCASSDKGTVHIFALKDTRLNRRSALARVGKVGPMIGQYVDSQWSLASF
TVPAESACICAFGRNTSKNVNSVIAICVDGTFHKYVFTPDGNCNREAFDVYLDICDDDDF

Sequence length

360

Interactions

View interactions

	KEGG		Reactome
	Autophagy - animal		Macroautophagy

Show/Hide Causal Diseases (3)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Neurodegeneration With Brain Iron Accumulation	neurodegeneration with brain iron accumulation 5	rs2065034268, rs1064793294, rs1569523502, rs1602538372, rs869312661, rs2065045334, rs1131691592, rs1569523468, rs387907328, rs1602539140, rs878855326, rs2065045650, rs1557083878, rs1569523565, rs387907329 View all (39 more)	N/A
Developmental Delay	global developmental delay	rs886041382	N/A
neurodegeneration with brain iron accumulation	Neurodegeneration with brain iron accumulation	rs1557083958	N/A

Show/Hide Unknown Diseases (3)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Infantile Spasms	infantile spasms	N/A	N/A	GenCC
Mental retardation	intellectual disability	N/A	N/A	ClinVar
Neurodevelopmental Disorders	X-linked complex neurodevelopmental disorder	N/A	N/A	GenCC

Show/Hide Text Mining Associations (41)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Attention Deficit and Disruptive Behavior Disorders	Associate	29322350
Basal Ganglia Diseases	Associate	39970510
Brain Diseases	Associate	26173968
Carcinoma Renal Cell	Associate	26208877
Cognition Disorders	Associate	34818117
Conversion Disorder	Associate	32387008
Dementia	Associate	23176820, 23687123
Demyelinating Diseases	Associate	32387008
Developmental Disabilities	Associate	23176820, 23687123, 32387008, 33037762, 34818117, 36350923
Dystonia	Associate	23176820, 23687123, 29082105, 36076926
Endometrial Neoplasms	Associate	26208877
Epilepsy	Associate	32387008, 33037762, 39970510
Epileptic Encephalopathy Early Infantile 3	Associate	29171013, 34818117
Genetic Diseases X Linked	Associate	23687123
Growth Retardation Developmental Delay Coarse Facies And Early Death	Associate	39970510
Hepatolenticular Degeneration	Inhibit	34769084
Heredodegenerative Disorders Nervous System	Associate	33636118
Idiopathic Hypersomnia	Associate	23687123
Immunologic Deficiency Syndromes	Associate	36076926
Intellectual Disability	Associate	26577041, 27159028, 29082105, 33037762, 33636118
Iron Deficiencies	Associate	36502619
Iron Overload	Associate	30169597, 34769084
Lysosomal Storage Diseases	Associate	30169597
Microphthalmia Syndromic 10	Associate	36076926
Mitochondrial Diseases	Associate	30169597, 34769084
Motor Skills Disorders	Associate	32387008
Muscle Hypertonia	Associate	29082105
Muscle Spasticity	Associate	36076926
Neoplasms	Associate	26208877
Nervous System Diseases	Associate	23176820
Neuroblastoma	Associate	34837396
Neurocognitive Disorders	Associate	26577041
Neurodegenerative Diseases	Associate	23687123, 26173968, 29082105, 30169597, 32387008, 34769084, 34818117, 34837396, 36502619
Neuroferritinopathy	Associate	23687123, 30169597, 36076926
Optic atrophy X linked	Associate	37819743
Pantothenate Kinase Associated Neurodegeneration	Associate	23176820, 28821231, 29082105, 32387008, 37834028, 39419454
Parkinson Disease Secondary	Associate	23176820, 23687123, 29082105, 32387008, 36076926
Rett Syndrome	Associate	29322350
Seizures	Associate	26577041, 29171013, 32387008
Sleep Wake Disorders	Associate	23687123
Tremor	Associate	29082105

WDR45 (WD repeat domain 45)