Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
23001
Gene name Gene Name - the full gene name approved by the HGNC.
WD repeat and FYVE domain containing 3
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
WDFY3
Synonyms (NCBI Gene) Gene synonyms aliases
ALFY, BCHS, MCPH18, ZFYVE25
Disease Acronyms (UniProt) Disease acronyms from UniProt database
MCPH18
Chromosome Chromosome number
4
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
4q21.23
Summary Summary of gene provided in NCBI Entrez Gene.
This gene encodes a phosphatidylinositol 3-phosphate-binding protein that functions as a master conductor for aggregate clearance by autophagy. This protein shuttles from the nuclear membrane to colocalize with aggregated proteins, where it complexes with
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs1553924800 G>A Pathogenic Missense variant, coding sequence variant, genic downstream transcript variant
rs1578183451 C>A Likely-pathogenic Coding sequence variant, genic downstream transcript variant, missense variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT051573 hsa-let-7e-5p CLASH 23622248
MIRT050648 hsa-miR-19a-3p CLASH 23622248
MIRT1489600 hsa-miR-1183 CLIP-seq
MIRT1489601 hsa-miR-1208 CLIP-seq
MIRT1489602 hsa-miR-1264 CLIP-seq
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0005515 Function Protein binding IPI 18083104, 20168092, 20417604, 22458338, 24668264, 25814554
GO:0005545 Function 1-phosphatidylinositol binding IDA 15292400
GO:0005635 Component Nuclear envelope IDA 15292400, 20417604
GO:0005654 Component Nucleoplasm IDA
GO:0005730 Component Nucleolus IDA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
617485 20751 ENSG00000163625
Protein
UniProt ID Q8IZQ1
Protein name WD repeat and FYVE domain-containing protein 3 (Autophagy-linked FYVE protein) (Alfy)
Protein function Required for selective macroautophagy (aggrephagy). Acts as an adapter protein by linking specific proteins destined for degradation to the core autophagic machinery members, such as the ATG5-ATG12-ATG16L E3-like ligase, SQSTM1 and LC3 (PubMed:2
PDB 3WIM , 6W9N
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF14844 PH_BEACH 2585 2656 PH domain associated with Beige/BEACH Domain
PF02138 Beach 2696 2976 Beige/BEACH domain Family
PF01363 FYVE 3449 3515 FYVE zinc finger Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in osteoclast and their mononuclear precursors (at protein level). {ECO:0000269|PubMed:20971078}.
Sequence
MNMVKRIMGRPRQEECSPQDNALGLMHLRRLFTELCHPPRHMTQKEQEEKLYMMLPVFNR
VFGNAPPNTMTEKFSDLLQFTTQVSRLMVTEIRRRASNKSTEAASRAIVQFLEINQSEEA
SRGWMLLTTINLLASSGQKTVDCMTTMSVPSTLVKCLYLFFDLPHVPEAVGGAQNELPLA
ERRGLLQKVFVQILVKLCSFVSPAEELAQKDDLQLLFSAITSWCPPYNLPWRKSAGEVLM
TISRHGLSVNVVKYIHEKECLSTCVQNMQQSDDLSPLEIVEMFAGLSCFLKDSSDVSQTL
LDDFRIWQGYNFLCDLLLRLEQAKEAESKDALKDLVNLITSLTTYGVSELKPAGITTGAP
FLLPGFAVPQPAGKGHSVRNVQAFAVLQNAFLKAKTSFLAQIILDAITNIYMADNANYFI
LESQHTLSQFAEKISKLPEVQNKYFEMLEFVVFSLNYIPCKELISVSILLKSSSSYHCSI
IAMKTLLKFTRHDYIFKDVFREVGLLEVMVNLLHKYAALLKDPTQALNEQGDSRNNSSVE
DQKHLALLVMETLTVLLQGSNTNAGIFREFGGARCAHNIVKYPQCRQHALMTIQQLVLSP
NGDDDMGTLLGLMHSAPPTELQLKTDILRALLSVLRESHRSRTVFRKVGGFVYITSLLVA
MERSLSCPPKNGWEKVNQNQVFELLHTVFCTLTAAMRYEPANSHFFKTEIQYEKLADAVR
FLGCFSDLRKISAMNVFPSNTQPFQRLLEEDVISIESVSPTLRHCSKLFIYLYKVATDSF
DSRAEQIPPCLTSESSLPSPWGTPALSRKRHAYHSVSTPPVYPPKNVADLKLHVTTSSLQ
SSDAVIIHPGAMLAMLDLLASVGSVTQPEHALDLQLAVANILQSLVHTERNQQVMCEAGL
HARLLQRCSAALADEDHSLHPPLQRMFERLASQALEPMVLREFLRLASPLNCGAWDKKLL
KQYRVHKPSSLSYEPEMRSSMITSLEGLGTDNVFSLHEDNHYRISKSLVKSAEGSTVPLT
RVKCLVSMTTPHDIRLHGSSVTPAFVEFDTSLEGFGCLFLPSLAPHNAPTNNTVTTGLID
GAVVSGIGSGERFFPPPSGLSYSSWFCIEHFSSPPNNHPVRLLTVVRRANSSEQHYVCLA
IVLSAKDRSLIVSTKEELLQNYVDDFSEESSFYEILPCCARFRCGELIIEGQWHHLVLVM
SKGMLKNSTAALYIDGQLVNTVKLHYVHSTPGGSGSANPPVVSTVYAYIGTPPAQRQIAS
LVWRLGPTHFLEEVLPSSNVTTIYELGPNYVGSFQAVCMPCKDAKSEGVVPSPVSLVPEE
KVSFGLYALSVSSLTVARIRKVYNKLDSKAIAKQLGISSHENATPVKLIHNSAGHLNGSA
RTIGAALIGYLGVRTFVPKPVATTLQYVGGAAAILGLVAMASDVEGLYAAVKALVCVVKS
NPLASKEMERIKGYQLLAMLLKKKRSLLNSHILHLTFSLVGTVDSGHETSIIPNSTAFQD
LLCDFEVWLHAPYELHLSLFEHFIELLTESSEASKNAKLMREFQLIPKLLLTLRDMSLSQ
PTIAAISNVLSFLLQGFPSSNDLLRFGQFISSTLPTFAVCEKFVVMEINNEEKLDTGTEE
EFGGLVSANLILLRNRLLDILLKLIYTSKEKTSINLQACEELVKTLGFDWIMMFMEEHLH
STTVTAAMRILVVLLSNQSILIKFKEGLSGGGWLEQTDSVLTNKIGTVLGFNVGRSAGGR
STVREINRDACHFPGFPVLQSFLPKHTNVPALYFLLMALFLQQPVSELPENLQVSVPVIS
CRSKQGCQFDLDSIWTFIFGVPASSGTVVSSIHNVCTEAVFLLLGMLRSMLTSPWQSEEE
GSWLREYPVTLMQFFRYLYHNVPDLASMWMSPDFLCALAATVFPFNIRPYSEMVTDLDDE
VGSPAEEFKAFAADTGMNRSQSEYCNVGTKTYLTNHPAKKFVFDFMRVLIIDNLCLTPAS
KQTPLIDLLLEASPERSTRTQQKEFQTYILDSVMDHLLAADVLLGEDASLPITSGGSYQV
LVNNVFYFTQRVVDKLWQGMFNKESKLLIDFIIQLIAQSKRRSQGLSLDAVYHCLNRTIL
YQFSRAHKTVPQQVALLDSLRVLTVNRNLILGPGNHDQEFISCLAHCLINLHVGSNVDGF
GLEAEARMTTWHIMIPSDIEPDGSYSQDISEGRQLLIKAVNRVWTELIHSKKQVLEELFK
VTLPVNERGHVDIATARPLIEEAALKCWQNHLAHEKKCISRGEALAPTTQSKLSRVSSGF
GLSKLTGSRRNRKESGLNKHSLSTQEISQWMFTHIAVVRDLVDTQYKEYQERQQNALKYV
TEEWCQIECELLRERGLWGPPIGSHLDKWMLEMTEGPCRMRKKMVRNDMFYNHYPYVPET
EQETNVASEIPSKQPETPDDIPQKKPARYRRAVSYDSKEYYMRLASGNPAIVQDAIVESS
EGEAAQQEPEHGEDTIAKVKGLVKPPLKRSRSAPDGGDEENQEQLQDQIAEGSSIEEEEK
TDNATLLRLLEEGEKIQHMYRCARVQGLDTSEGLLLFGKEHFYVIDGFTMTATREIRDIE
TLPPNMHEPIIPRGARQGPSQLKRTCSIFAYEDIKEVHKRRYLLQPIAVEVFSGDGRNYL
LAFQKGIRNKVYQRFL
AVVPSLTDSSESVSGQRPNTSVEQGSGLLSTLVGEKSVTQRWER
GEISNFQYLMHLNTLAGRSYNDLMQYPVFPWILADYDSEEVDLTNPKTFRNLAKPMGAQT
DERLAQYKKRYKDWEDPNGETPAYHYGTHYSSAMIVASYLVRMEPFTQIFLRLQGGHFDL
ADRMFHSVREAWYSASKHNMADVKELIPEFFYLPEFLFNSNNFDLGCKQNGTKLGDVILP
PWAKGDPREFIRVHREALECDYVSAHLHEWIDLIFGYKQQGPAAVEAVNVFHHLFYEGQV
DIYNINDPLKETATIGFINNFGQIPKQLFKKPHPPK
RVRSRLNGDNAGISVLPGSTSDKI
FFHHLDNLRPSLTPVKELKEPVGQIVCTDKGILAVEQNKVLIPPTWNKTFAWGYADLSCR
LGTYESDKAMTVYECLSEWGQILCAICPNPKLVITGGTSTVVCVWEMGTSKEKAKTVTLK
QALLGHTDTVTCATASLAYHIIVSGSRDRTCIIWDLNKLSFLTQLRGHRAPVSALCINEL
TGDIVSCAGTYIHVWSINGNPIVSVNTFTGRSQQIICCCMSEMNEWDTQNVIVTGHSDGV
VRFWRMEFLQVPETPAPEPAEVLEMQEDCPEAQIGQEAQDEDSSDSEADEQSISQDPKDT
PSQPSSTSHRPRAASCRATAAWCTDSGSDDSRRWSDQLSLDEKDGFIFVNYSEGQTRAHL
QGPLSHPHPNPIEVRNYSRLKPGYRWERQLVFRSKLTMHTAFDRKDNAHPAEVTALGISK
DHSRILVGDSRGRVFSWSVSDQPGRSAADHWVKDEGGDSCSGCSVRFSLTERRHHCRNCG
QLFCQKCSRFQSEIKRLKISSPVRVCQNCYYNLQH
ERGSEDGPRNC
Sequence length 3526
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  
  Autophagy - animal  
Associated diseases Disease information provided by ClinVar, GenCC, and GWAS databases.
Causal
Disease term Disease name dbSNP ID References
Mental retardation Mild Mental Retardation, Moderate intellectual disability rs5742905, rs267607136, rs267607137, rs2131714307, rs267607038, rs267607042, rs80338685, rs137853127, rs80338815, rs28940893, rs387906309, rs121908096, rs121908099, rs587784365, rs121918315
View all (1024 more)
Microcephaly Microcephaly, MICROCEPHALY 18, PRIMARY, AUTOSOMAL DOMINANT rs397704721, rs267607176, rs267607177, rs397704725, rs267606717, rs267606718, rs199422202, rs121434311, rs199422203, rs199422126, rs387906274, rs121434305, rs199422125, rs199422135, rs189678019
View all (280 more)
28191889, 27008544
Neurodevelopmental disorders Neurodevelopmental Disorders rs869312846, rs869312840, rs869312848, rs869312849, rs869312845, rs886041956, rs1064795110, rs1555762734, rs1555764992, rs1568512728, rs1568532361, rs1595472741, rs1595472764, rs1595476797, rs1016320330
View all (2 more)
28191889
Unknown
Disease term Disease name Evidence References Source
Autism Spectrum Disorder autism spectrum disorder GenCC
Neurodevelopmental Disorders complex neurodevelopmental disorder GenCC
Schizophrenia Schizophrenia GWAS
Associations from Text Mining
Disease Name Relationship Type References
Ataxia Associate 34130600
Autism Spectrum Disorder Associate 27824329
Autistic Disorder Associate 27824329, 30564305
Brain Diseases Associate 34130600
Carcinoma Ductal Associate 30959550
Cerebral Hemorrhage Associate 30836997
Chediak Higashi Syndrome Associate 34130600
Colorectal Neoplasms Associate 23045723
Congenital Hereditary and Neonatal Diseases and Abnormalities Associate 34130600
Esophageal Neoplasms Associate 30972633, 32536038