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	11152
Gene name	WD repeat domain 45
Gene symbol	WDR45
Synonyms (NCBI Gene)	JM5NBIA4NBIA5WDRX1WIPI-4WIPI4
Chromosome	X
Chromosome location	Xp11.23
Summary	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

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

457

Show/Hide Causal Diseases (14)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Autism	Likely pathogenic	rs1602540235	RCV001004010
Basal ganglia calcification	Pathogenic	rs1602540581	RCV001004011
Developmental disorder	Pathogenic	rs2520266090	RCV003127353
Dystonic disorder	Pathogenic	rs1602540581	RCV001004011
Global developmental delay	Pathogenic; Likely pathogenic	rs886041382, rs1602540235, rs2520266854	RCV001255400 RCV001004010 RCV001255399
Intellectual disability	Pathogenic	rs2065030871, rs781998959	RCV001255354 RCV001260892
Neurodegeneration with brain iron accumulation	Pathogenic	rs1557083958	RCV000845069
Neurodegeneration with brain iron accumulation 5	Likely pathogenic; Pathogenic	rs2065027151, rs2147815209, rs2147814810, rs2147815120, rs2147816498, rs2147817379, rs2147817417, rs2147815172, rs2147815446, rs2147814944, rs2147814859, rs2147816332, rs2147814431, rs2147817625, rs2147816654 View all (97 more)	RCV001323126 RCV001378504 RCV001389746 RCV001385179 RCV001382098 RCV001387145 RCV001389596 RCV001542248 RCV001775306 RCV001784033 RCV001799571 RCV003738102 RCV001889113 RCV001973305 RCV002003820 RCV001882116 RCV001986444 RCV002024856 RCV002246817 RCV002246818 RCV002272799 RCV002288379 RCV002290225 RCV003064720 RCV003084933 RCV002810424 RCV000195088 RCV000194492 RCV000195151 RCV000194153 RCV000477948 RCV002903472 RCV003002506 RCV003025183 RCV003049749 RCV003036874 RCV000209935 RCV003134786 RCV003149136 RCV003326676 RCV003152840 RCV003153196 RCV000234791 RCV000578469 RCV001388846 RCV000705613 RCV005090332 RCV000850623 RCV003311579 RCV003322679 RCV003387493 RCV003572867 RCV003572959 RCV003573565 RCV003576090 RCV003735129 RCV003735150 RCV003735155 RCV003735160 RCV003735189 RCV003735260 RCV003735329 RCV003735366 RCV003735378 RCV003985185 RCV000417260 RCV001242357 RCV000554794 RCV000538621 RCV000578356 RCV000578306 RCV002248813 RCV000034828 RCV000034829 RCV000034830 RCV000034831 RCV000034832 RCV001809706 RCV000627053 RCV000650354 RCV000650353 RCV000689103 RCV000735636 RCV000695691 RCV000687313 RCV000692175 RCV000714536 RCV000760207 RCV001194319 RCV000787276 RCV000797757 RCV000820924 RCV000792874 RCV000791938 RCV000804443 RCV000816156 RCV000825010 RCV000850624 RCV000986092 RCV000990817 RCV000990818 RCV000990819 RCV000990820 RCV003890154 RCV001004757 RCV001054071 RCV001052729 RCV001062938 RCV001042261 RCV003128264 RCV001214756 RCV001197735 RCV001214992 RCV001218190 RCV001204597 RCV001210870 RCV001235930 RCV001252632 RCV001253570 RCV001253381 RCV001253656 RCV001254141
Oculocutaneous albinism type 7	Pathogenic	rs886041382	RCV003883145
Optic atrophy 2	Likely pathogenic	rs2520264339, rs2520266803	RCV003147747 RCV003147748
See cases	Pathogenic; Likely pathogenic	rs387907328, rs781978699	RCV002251946 RCV001420217
Seizure	Likely pathogenic; Pathogenic	rs1064793294, rs1602540235	RCV005624402 RCV001004010
WDR45-related disorder	Pathogenic	rs1557083878, rs2520261696	RCV003402408 RCV003410586
X-linked cerebral-cerebellar-coloboma syndrome syndrome	Likely pathogenic; Pathogenic	rs797046101, rs1569523544	RCV000679876 RCV000679878

Show/Hide Unknown Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Malignant tumor of urinary bladder	Benign	rs782457722	RCV005896691
Migraine, familial hemiplegic, 1	Uncertain significance	rs2520259129	RCV003233045
Nonpapillary renal cell carcinoma	Uncertain significance	rs1557083823, rs781805068	RCV005911271 RCV005925394
Sarcoma	Likely benign	rs371546812	RCV005898849
Thyroid cancer, nonmedullary, 1	Uncertain significance; Conflicting classifications of pathogenicity	rs1557083823, rs2065029228, rs1569523500	RCV005911272 RCV005931763 RCV005901822

Show/Hide Text Mining Associations (41)

Disease Name	Relationship Type	References
Associations from Text MiningDisease 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)