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

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	284403
Gene name	WD repeat domain 62
Gene symbol	WDR62
Synonyms (NCBI Gene)	C19orf14MCPH2
Chromosome	19
Chromosome location	19q13.12
Summary	This gene is proposed to play a role in cerebral cortical development. Mutations in this gene have been associated with microencephaly, cortical malformations, and cognitive disability. Alternative splicing results in multiple transcript variants. [provid

Show/Hide all (68)

SNP ID	Visualize variation	Clinical significance	Consequence
rs2301734	G>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign, benign-likely-benign	Synonymous variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant
rs35811023	C>G	Benign-likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, missense variant
rs117887683	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, synonymous variant
rs137919897	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, genic upstream transcript variant, upstream transcript variant
rs139371621	C>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, non coding transcript variant, synonymous variant, coding sequence variant
rs139460397	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant, synonymous variant, intron variant
rs139749569	T>C	Conflicting-interpretations-of-pathogenicity, benign-likely-benign	Missense variant, genic downstream transcript variant, coding sequence variant
rs139946168	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs141344823	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, intron variant, coding sequence variant
rs146180208	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, coding sequence variant
rs146485488	G>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant
rs147652186	C>A,G	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, coding sequence variant
rs147875659	G>A,C,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, non coding transcript variant, stop gained, coding sequence variant
rs148415080	C>T	Benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs148667984	C>T	Uncertain-significance, benign, conflicting-interpretations-of-pathogenicity	Genic upstream transcript variant, non coding transcript variant, synonymous variant, upstream transcript variant, coding sequence variant
rs199736219	G>A	Pathogenic	Genic downstream transcript variant, splice donor variant
rs201053854	G>T	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs201363122	C>T	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, coding sequence variant, missense variant
rs202109439	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs267607176	G>C	Pathogenic	Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs267607177	C>T	Pathogenic	Stop gained, 5 prime UTR variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant
rs373906889	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant
rs376633424	C>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, stop gained
rs377731205	C>T	Pathogenic	Genic downstream transcript variant, coding sequence variant, missense variant
rs387907082	G>A	Pathogenic	Coding sequence variant, upstream transcript variant, non coding transcript variant, genic upstream transcript variant, missense variant
rs387907083	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, genic upstream transcript variant, missense variant, intron variant
rs387907084	G>A	Pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs397704721	TGCC>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant
rs397704725	GCCAAGAGCCTGCCCTG>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant
rs587776899	->T	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs587776900	->C	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs587776901	T>-	Pathogenic	Genic upstream transcript variant, frameshift variant, coding sequence variant, non coding transcript variant
rs587784542	C>T	Likely-pathogenic	Upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs587784543	G>A	Likely-pathogenic	5 prime UTR variant, non coding transcript variant, missense variant, coding sequence variant, genic upstream transcript variant
rs587784546	->AAAGCAT	Pathogenic	5 prime UTR variant, frameshift variant, non coding transcript variant, coding sequence variant, intron variant
rs587784548	G>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, genic downstream transcript variant, missense variant
rs587784549	C>G	Pathogenic	Stop gained, coding sequence variant, genic downstream transcript variant
rs587784553	G>A	Pathogenic	Genic upstream transcript variant, splice donor variant
rs587784554	A>G	Likely-pathogenic	Genic downstream transcript variant, intron variant
rs587784558	C>A	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs757091694	T>C	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs757294519	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, genic downstream transcript variant, intron variant
rs764201220	AGAG>-,AG	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant
rs765451882	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic upstream transcript variant, coding sequence variant, upstream transcript variant, non coding transcript variant, intron variant
rs769688376	C>A	Pathogenic	Stop gained, genic upstream transcript variant, coding sequence variant, upstream transcript variant, non coding transcript variant
rs773948810	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, genic downstream transcript variant
rs776948954	A>C	Conflicting-interpretations-of-pathogenicity	Missense variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs778207666	G>A	Uncertain-significance, pathogenic	Genic upstream transcript variant, intron variant, coding sequence variant, synonymous variant, non coding transcript variant
rs779093591	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, genic upstream transcript variant, coding sequence variant, non coding transcript variant
rs797046109	C>-	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs863223322	A>-	Pathogenic	Frameshift variant, intron variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs863223377	T>C	Pathogenic	Genic upstream transcript variant, missense variant, upstream transcript variant, coding sequence variant, 5 prime UTR variant, non coding transcript variant
rs886041863	T>G	Pathogenic	Splice donor variant, downstream transcript variant, genic downstream transcript variant
rs1006898944	C>T	Pathogenic	Stop gained, genic downstream transcript variant, coding sequence variant
rs1064793462	CA>GTGGTCTGAG	Pathogenic	Coding sequence variant, inframe indel, genic downstream transcript variant, stop gained
rs1064797237	C>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs1213710245	->T	Pathogenic	Frameshift variant, non coding transcript variant, genic upstream transcript variant, upstream transcript variant, coding sequence variant
rs1265252597	G>A	Pathogenic	Intron variant, coding sequence variant, non coding transcript variant, genic upstream transcript variant, 5 prime UTR variant, stop gained
rs1379578836	C>A,G,T	Likely-pathogenic	Genic upstream transcript variant, coding sequence variant, non coding transcript variant, missense variant
rs1555723585	->AGCCATCCACTCCCCAGCTCCGC	Pathogenic	Intron variant, coding sequence variant, frameshift variant, genic downstream transcript variant
rs1555725014	->C	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1568334868	ACAGGTCTCCCT>-	Likely-pathogenic	Upstream transcript variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant, intron variant, splice acceptor variant
rs1599760058	C>-	Pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1599774265	C>-	Likely-pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, genic upstream transcript variant, intron variant
rs1599805729	->GCTG	Pathogenic	Genic upstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1599841026	C>T	Pathogenic	Coding sequence variant, stop gained, genic downstream transcript variant
rs1599851667	->C	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1599852762	->GTCCCCAC	Likely-pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant

Show/Hide all (8)

miRTarBase ID	miRNA	Experiments	Reference
MIRT016504	hsa-miR-193b-3p	Microarray	20304954
MIRT045652	hsa-miR-149-5p	CLASH	23622248
MIRT045108	hsa-miR-186-5p	CLASH	23622248
MIRT040399	hsa-miR-615-3p	CLASH	23622248
MIRT039350	hsa-miR-542-5p	CLASH	23622248
MIRT039175	hsa-miR-769-5p	CLASH	23622248
MIRT037077	hsa-miR-877-3p	CLASH	23622248
MIRT052764	hsa-miR-1260b	CLASH	23622248

Show/Hide all (21)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000922	Component	Spindle pole	IDA	20890278, 20890279
GO:0000922	Component	Spindle pole	IEA
GO:0002052	Process	Positive regulation of neuroblast proliferation	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 25416956, 26297806, 26496610, 28089251, 32296183, 32707033, 35271311, 36931259
GO:0005634	Component	Nucleus	IDA	20729831
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	26297806
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005856	Component	Cytoskeleton	IEA
GO:0007052	Process	Mitotic spindle organization	IMP	24388750
GO:0007099	Process	Centriole replication	IMP	26297806
GO:0007399	Process	Nervous system development	IEA
GO:0021987	Process	Cerebral cortex development	IMP	20729831
GO:0022008	Process	Neurogenesis	IMP	20890278
GO:0034451	Component	Centriolar satellite	IDA
GO:0045664	Process	Regulation of neuron differentiation	IEA
GO:0046605	Process	Regulation of centrosome cycle	IEA
GO:2001224	Process	Positive regulation of neuron migration	IEA

MIM	HGNC	e!Ensembl
613583	24502	ENSG00000075702

O43379

Protein name

WD repeat-containing protein 62

Protein function

Required for cerebral cortical development. Plays a role in neuronal proliferation and migration (PubMed:20729831, PubMed:20890278). Plays a role in mother-centriole-dependent centriole duplication; the function also seems to involve CEP152, CDK

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00400	WD40	101 → 141	WD domain, G-beta repeat	Repeat
PF00400	WD40	348 → 387	WD domain, G-beta repeat	Repeat
PF00400	WD40	399 → 441	WD domain, G-beta repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Present in fetal brain, enriched within the ventricular and subventricular zone (at protein level). In the embryonic brain it is expressed in mitotic neural precursor cells. {ECO:0000269|PubMed:20890279}.

Sequence

MAAVGSGGYARNDAGEKLPSVMAGVPARRGQSSPPPAPPICLRRRTRLSTASEETVQNRV
SLEKVLGITAQNSSGLTCDPGTGHVAYLAGCVVVILDPKENKQQHIFNTARKSLSALAFS
PDGKYIVTGENGHRPAVRIWDVEEKNQVAEMLGHKYGVACVAFSPNMKHIVSMGYQHDMV
LNVWDWKKDIVVASNKVSCRVIALSFSEDSSYFVTVGNRHVRFWFLEVSTETKVTSTVPL
VGRSGILGELHNNIFCGVACGRGRMAGSTFCVSYSGLLCQFNEKRVLEKWINLKVSLSSC
LCVSQELIFCGCTDGIVRIFQAHSLHYLANLPKPHYLGVDVAQGLEPSFLFHRKAEAVYP
DTVALTFDPIHQWLSCVYKDHSIYIWDVKDINRVGKVWSELFHSSYVWNVEVYPEFEDQR
ACLPSGSFLTCSSDNTIRFWNLDSSPDSHWQKNIFSNTLLKVVYVENDIQHLQDMSHFPD
RGSENGTPMDVKAGVRVMQVSPDGQHLASGDRSGNLRIHELHFMDELVKVEAHDAEVLCL
EYSKPETGLTLLASASRDRLIHVLNVEKNYNLEQTLDDHSSSITAIKFAGNRDIQMISCG
ADKSIYFRSAQQGSDGLHFVRTHHVAEKTTLYDMDIDITQKYVAVACQDRNVRVYNTVNG
KQKKCYKGSQGDEGSLLKVHVDPSGTFLATSCSDKSISVIDFYSGECIAKMFGHSEIITS
MKFTYDCHHLITVSGDSCVFIWHLGPEITNCMKQHLLEIDHRQQQQHTNDKKRSGHPRQD
TYVSTPSEIHSLSPGEQTEDDLEEECEPEEMLKTPSKDSLDPDPRCLLTNGKLPLWAKRL
LGDDDVADGLAFHAKRSYQPHGRWAERAGQEPLKTILDAQDLDCYFTPMKPESLENSILD
SLEPQSLASLLSESESPQEAGRGHPSFLPQQKESSEASELILYSLEAEVTVTGTDSQYCR
KEVEAGPGDQQGDSYLRVSSDSPKDQSPPEDSGESEADLECSFAAIHSPAPPPDPAPRFA
TSLPHFPGCAGPTEDELSLPEGPSVPSSSLPQTPEQEKFLRHHFETLTESPCRALGDVEA
SEAEDHFFNPRLSISTQFLSSLQKASRFTHTFPPRATQCLVKSPEVKLMDRGGSQPRAGT
GYASPDRTHVLAAGKAEETLEAWRPPPPCLTSLASCVPASSVLPTDRNLPTPTSAPTPGL
AQGVHAPSTCSYMEATASSRARISRSISLGDSEGPIVATLAQPLRRPSSVGELASLGQEL
QAITTATTPSLDSEGQEPALRSWGNHEARANLRLTLSSACDGLLQPPVDTQPGVTVPAVS
FPAPSPVEESALRLHGSAFRPSLPAPESPGLPAHPSNPQLPEARPGIPGGTASLLEPTSG
ALGLLQGSPARWSEPWVPVEALPPSPLELSRVGNILHRLQTTFQEALDLYRVLVSSGQVD
TGQQQARTELVSTFLWIHSQLEAECLVGTSVAPAQALPSPGPPSPPTLYPLASPDLQALL
EHYSELLVQAVRRKARGH

Sequence length

1518

Interactions

View interactions

399

Show/Hide Causal Diseases (10)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Abnormal cerebral morphology	Likely pathogenic	rs2145591077	RCV002275460
Abnormality of neuronal migration	Pathogenic	rs863223377	RCV000201429
Abnormality of the nervous system	Pathogenic	rs1417437683	RCV001814400
Autosomal recessive primary microcephaly	Likely pathogenic	rs2513393044	RCV003123411
Intellectual disability	Pathogenic; Likely pathogenic	rs754976942, rs1973468140	RCV001291204 RCV001291203
Microcephaly 2, primary, autosomal recessive, with or without cortical malformations	Likely pathogenic; Pathogenic	rs1970564827, rs2145706114, rs2145516989, rs769137869, rs369923535, rs2145528028, rs2145795692, rs2145586826, rs397704721, rs267607176, rs267607177, rs397704725, rs1234259290, rs750117864, rs587784553 View all (44 more)	RCV001331597 RCV001780405 RCV001785141 RCV001784035 RCV005922525 RCV001807904 RCV001808236 RCV001822015 RCV000000057 RCV000000059 RCV000000060 RCV000000061 RCV002052105 RCV003126213 RCV000147952 RCV000147962 RCV000147928 RCV000147941 RCV000147953 RCV002289365 RCV002471486 RCV002470552 RCV003152802 RCV000194814 RCV002790027 RCV005021813 RCV003134788 RCV003149133 RCV000763424 RCV003334462 RCV003486347 RCV003494091 RCV004018309 RCV004595302 RCV000024029 RCV000024030 RCV000024031 RCV000024032 RCV000024033 RCV000024034 RCV000024035 RCV000024036 RCV000500750 RCV000504101 RCV000501183 RCV004576959 RCV000786041 RCV000786042 RCV001007663 RCV001255785 RCV003985097 RCV001009331 RCV001072152 RCV001253709 RCV001255843 RCV001255769 RCV001507261 RCV001507262 RCV001507260
Primary microcephaly type 2	Pathogenic	rs387907083	RCV001250231
Skraban-Deardorff syndrome	Likely pathogenic	rs2513454904	RCV003989395
Squamous cell lung carcinoma	Pathogenic	rs1284984423	RCV005909115
WDR62-related disorder	Pathogenic; Likely pathogenic	rs757827840, rs2513744398	RCV003336451 RCV003335847

Show/Hide Unknown Diseases (20)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Acute myeloid leukemia	Benign; Likely benign	rs12327568, rs182467995	RCV005888282 RCV005888274
Adrenocortical carcinoma, hereditary	-	rs1972529051	RCV005930180
Cervical cancer	Benign; Likely benign	rs182467995	RCV005888276
Clear cell carcinoma of kidney	Conflicting classifications of pathogenicity	rs139946168	RCV005892401
Colon adenocarcinoma	Benign; Likely benign	rs182467995	RCV005888273
Familial cancer of breast	Benign; Likely benign; Uncertain significance	rs138928852, rs182467995, rs772078670, rs146898747	RCV005888270 RCV005888272 RCV005932080 RCV005899957
Gastric cancer	Likely benign; Benign	rs114744677, rs138928852, rs182467995, rs146898747	RCV005914723 RCV005888271 RCV005888277 RCV005899959
Hepatocellular carcinoma	Benign; Likely benign	rs146898747	RCV005899958
Lung cancer	Likely benign; Benign	rs114744677, rs182467995	RCV005914724 RCV005888281
Lymphoma	Benign; Likely benign	rs182467995	RCV005888278
Malignant tumor of esophagus	Conflicting classifications of pathogenicity	rs757294519	RCV005889886
Microcephaly	Uncertain significance	rs1599851829	RCV000850356
Microcephaly, cortical malformations, and intellectual disability	Uncertain significance	rs769860430, rs769679657, rs199678831	RCV002221227 RCV002221228 RCV002221226
Nonpapillary renal cell carcinoma	Benign; Likely benign	rs182467995	RCV005888275
Ovarian serous cystadenocarcinoma	Benign; Likely benign; Conflicting classifications of pathogenicity	rs182467995, rs757294519	RCV005888279 RCV005889887
Primary Microcephaly 2 With or Without Cortical Malformations	Conflicting classifications of pathogenicity	rs373693641, rs797046108, rs147077663	RCV000392212 RCV000273209 RCV000299793 RCV000362050
Primary Microcephaly, Recessive	Uncertain significance	rs769860430, rs769679657, rs199678831	RCV000383411 RCV000293868 RCV000363841
Sarcoma	Likely benign	rs114744677	RCV005914722
Thymoma	Benign; Likely benign	rs182467995	RCV005888280
Uterine corpus endometrial carcinoma	Benign	rs115661549	RCV005917928

Show/Hide Text Mining Associations (24)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Agenesis of Corpus Callosum	Associate	24228726
Autosomal Recessive Primary Microcephaly	Associate	10677332, 21961505, 24228726, 24479948, 26297806, 28377545, 30021525, 32677750, 33921653, 34068194, 34137788, 34402213, 37272619
Brain Diseases	Associate	34137788, 37272619
Breast Neoplasms	Associate	30091641
Carcinogenesis	Associate	35758246
Central Nervous System Vascular Malformations	Associate	28377545
Cerebellar Hypoplasia	Associate	24228726
Colorectal Neoplasms	Associate	35758246
Congenital Abnormalities	Associate	33921653
Developmental Disabilities	Associate	24479948, 33921653
Fetal Alcohol Spectrum Disorders	Associate	37272619
Gerstmann Syndrome	Associate	28377545
Head and Neck Neoplasms	Associate	28377545
Hippocampal Sclerosis	Associate	24228726
Intellectual Disability	Associate	30500859
Lissencephaly	Associate	30091641
Malformations of Cortical Development	Associate	23341463, 25385192, 33921653
Microcephaly	Associate	20890278, 23341463, 24228726, 25385192, 25501809, 26297806, 28377545, 30021525, 30091641, 32677750, 33921653, 34068194, 37272619
Microcephaly Primary Autosomal Recessive 2	Associate	24228726, 33921653
Microcephaly with Simplified Gyral Pattern	Associate	20890278
Neoplasms	Stimulate	34306258
Neoplasms	Associate	35758246
Neurologic Manifestations	Associate	34068194
Polymicrogyria	Associate	21834044, 33818783

WDR62 (WD repeat domain 62)