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.	57728
Gene name Gene Name - the full gene name approved by the HGNC.	WD repeat domain 19
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	WDR19
Synonyms (NCBI Gene) Gene synonyms aliases	ATD5, CED4, CFAP66, DYF-2, FAP66, IFT144, NPHP13, ORF26, Oseg6, PWDMP, SPGF72, SRTD5
Chromosome Chromosome number	4
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	4p14
Summary Summary of gene provided in NCBI Entrez Gene.	The protein encoded by this gene is a member of the WD (tryptophan-aspartic acid) repeat family, which is a large family of structurally-related proteins known to participate in a wide range of cellular processes. Each WD repeat typically contains about 4

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SNP ID	Visualize variation	Clinical significance	Consequence
rs76599296	C>G	Conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs79436363	G>A	Pathogenic, uncertain-significance, pathogenic-likely-pathogenic	Missense variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs141039852	G>A,C	Conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, non coding transcript variant, coding sequence variant
rs187546086	A>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs199904529	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant
rs200266424	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs200339331	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, synonymous variant, non coding transcript variant
rs201597047	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs201685269	G>A,C	Likely-pathogenic	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs201963605	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, missense variant
rs374400438	A>G	Pathogenic	Splice acceptor variant
rs375644378	A>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs377160857	G>A	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs387906980	T>C	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs387906981	C>A,T	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, synonymous variant, genic downstream transcript variant
rs387906982	T>C	Pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant, non coding transcript variant
rs387906983	T>G	Pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs587777348	T>-,TT	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant, frameshift variant
rs587777349	G>C	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant
rs587777350	C>T	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs587777351	G>A	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs587777352	G>A,T	Pathogenic	Splice donor variant, genic downstream transcript variant
rs745603321	G>A,C	Pathogenic	Missense variant, non coding transcript variant, coding sequence variant, genic downstream transcript variant
rs747165335	ACGG>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant, genic downstream transcript variant
rs748656635	->A	Pathogenic, uncertain-significance	Frameshift variant, non coding transcript variant, coding sequence variant
rs751386429	G>A,T	Likely-pathogenic	Missense variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant
rs757992911	C>-	Conflicting-interpretations-of-pathogenicity	Intron variant
rs771148519	C>G	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs772599282	C>T	Pathogenic	Coding sequence variant, non coding transcript variant, genic downstream transcript variant, stop gained
rs774658703	A>G,T	Pathogenic	Splice acceptor variant
rs776687469	G>C,T	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs780847651	T>C	Likely-pathogenic	Splice donor variant
rs786204852	T>A	Pathogenic	Coding sequence variant, non coding transcript variant, 5 prime UTR variant, missense variant
rs786205114	->A	Pathogenic	Genic downstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs886039814	C>G	Likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs886041912	G>A	Pathogenic	Splice donor variant
rs1064796985	G>A	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs1064796986	T>C	Likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs1191056931	G>A,C	Pathogenic	Genic downstream transcript variant, splice donor variant
rs1215108056	G>C	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1237494778	T>C	Likely-pathogenic	Missense variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1327583103	G>A	Pathogenic	Splice acceptor variant
rs1451698951	G>A	Pathogenic	Missense variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1553905326	T>C	Pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553907440	G>-	Pathogenic	Non coding transcript variant, coding sequence variant, frameshift variant
rs1553918403	A>C	Pathogenic	Splice acceptor variant, genic downstream transcript variant
rs1560541088	ATTGTTAGAGAGACCCAGTCTCTGGATGGAGCCAAAA>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, non coding transcript variant, coding sequence variant
rs1577822861	T>G	Pathogenic	Intron variant, stop gained, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs1577823005	->A	Likely-pathogenic	Intron variant, 5 prime UTR variant, frameshift variant, non coding transcript variant, coding sequence variant
rs1577943445	G>A	Likely-pathogenic	Stop gained, non coding transcript variant, coding sequence variant

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miRTarBase ID	miRNA	Experiments	Reference
MIRT017813	hsa-miR-335-5p	Microarray	18185580
MIRT049394	hsa-miR-92a-3p	CLASH	23622248
MIRT1489821	hsa-miR-1185	CLIP-seq
MIRT1489822	hsa-miR-132	CLIP-seq
MIRT1489823	hsa-miR-148a	CLIP-seq
MIRT1489824	hsa-miR-148b	CLIP-seq
MIRT1489825	hsa-miR-152	CLIP-seq
MIRT1489826	hsa-miR-1914	CLIP-seq
MIRT1489827	hsa-miR-212	CLIP-seq
MIRT1489828	hsa-miR-2467-3p	CLIP-seq
MIRT1489829	hsa-miR-3148	CLIP-seq
MIRT1489830	hsa-miR-3190	CLIP-seq
MIRT1489831	hsa-miR-3678-3p	CLIP-seq
MIRT1489832	hsa-miR-3679-5p	CLIP-seq
MIRT1489833	hsa-miR-574-5p	CLIP-seq
MIRT1489834	hsa-miR-626	CLIP-seq
MIRT1489835	hsa-miR-942	CLIP-seq
MIRT2368101	hsa-miR-3713	CLIP-seq
MIRT2368102	hsa-miR-4742-3p	CLIP-seq
MIRT2368103	hsa-miR-4768-5p	CLIP-seq
MIRT2368104	hsa-miR-579	CLIP-seq
MIRT2661616	hsa-miR-106a	CLIP-seq
MIRT2661617	hsa-miR-106b	CLIP-seq
MIRT2661618	hsa-miR-17	CLIP-seq
MIRT2661619	hsa-miR-185	CLIP-seq
MIRT2661620	hsa-miR-20a	CLIP-seq
MIRT2661621	hsa-miR-20b	CLIP-seq
MIRT2661622	hsa-miR-3661	CLIP-seq
MIRT2661623	hsa-miR-3678-5p	CLIP-seq
MIRT2661624	hsa-miR-371-3p	CLIP-seq
MIRT2661625	hsa-miR-3978	CLIP-seq
MIRT2661626	hsa-miR-4254	CLIP-seq
MIRT2661627	hsa-miR-4306	CLIP-seq
MIRT2661628	hsa-miR-4644	CLIP-seq
MIRT2661629	hsa-miR-4715-3p	CLIP-seq
MIRT2368103	hsa-miR-4768-5p	CLIP-seq
MIRT2661630	hsa-miR-4795-5p	CLIP-seq
MIRT2661631	hsa-miR-519d	CLIP-seq
MIRT2368104	hsa-miR-579	CLIP-seq
MIRT2661632	hsa-miR-619	CLIP-seq
MIRT2661633	hsa-miR-631	CLIP-seq
MIRT2661634	hsa-miR-93	CLIP-seq
MIRT2661616	hsa-miR-106a	CLIP-seq
MIRT2661617	hsa-miR-106b	CLIP-seq
MIRT2661618	hsa-miR-17	CLIP-seq
MIRT2661619	hsa-miR-185	CLIP-seq
MIRT2661620	hsa-miR-20a	CLIP-seq
MIRT2661621	hsa-miR-20b	CLIP-seq
MIRT2661622	hsa-miR-3661	CLIP-seq
MIRT2661623	hsa-miR-3678-5p	CLIP-seq
MIRT2661624	hsa-miR-371-3p	CLIP-seq
MIRT2661625	hsa-miR-3978	CLIP-seq
MIRT2661626	hsa-miR-4254	CLIP-seq
MIRT2661627	hsa-miR-4306	CLIP-seq
MIRT2661628	hsa-miR-4644	CLIP-seq
MIRT2661629	hsa-miR-4715-3p	CLIP-seq
MIRT2661630	hsa-miR-4795-5p	CLIP-seq
MIRT2661631	hsa-miR-519d	CLIP-seq
MIRT2661632	hsa-miR-619	CLIP-seq
MIRT2661633	hsa-miR-631	CLIP-seq
MIRT2661634	hsa-miR-93	CLIP-seq

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GO ID	Ontology	Definition	Evidence	Reference
GO:0000902	Process	Cell morphogenesis	IEA
GO:0001701	Process	In utero embryonic development	IEA
GO:0001750	Component	Photoreceptor outer segment	IEA
GO:0005515	Function	Protein binding	IPI	27173435, 27932497, 28514442, 29220510, 33961781
GO:0005737	Component	Cytoplasm	IEA
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IEA
GO:0005929	Component	Cilium	NAS	27806291
GO:0005929	Component	Cilium	TAS
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0008406	Process	Gonad development	IEA
GO:0030030	Process	Cell projection organization	IEA
GO:0030326	Process	Embryonic limb morphogenesis	IEA
GO:0030991	Component	Intraciliary transport particle A	IBA
GO:0030991	Component	Intraciliary transport particle A	IDA	20889716, 27932497
GO:0030991	Component	Intraciliary transport particle A	IEA
GO:0030991	Component	Intraciliary transport particle A	IPI	27173435
GO:0031076	Process	Embryonic camera-type eye development	IEA
GO:0031514	Component	Motile cilium	IEA
GO:0031514	Component	Motile cilium	ISS
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0035721	Process	Intraciliary retrograde transport	IBA
GO:0035721	Process	Intraciliary retrograde transport	IEA
GO:0035721	Process	Intraciliary retrograde transport	IMP	20889716
GO:0035721	Process	Intraciliary retrograde transport	NAS	27806291
GO:0042471	Process	Ear morphogenesis	IEA
GO:0042995	Component	Cell projection	IEA
GO:0043113	Process	Receptor clustering	IEA
GO:0044782	Process	Cilium organization	IEA
GO:0048701	Process	Embryonic cranial skeleton morphogenesis	IEA
GO:0050877	Process	Nervous system process	IEA
GO:0055123	Process	Digestive system development	IEA
GO:0060271	Process	Cilium assembly	IBA
GO:0060271	Process	Cilium assembly	IEA
GO:0060271	Process	Cilium assembly	NAS	27806291
GO:0060831	Process	Smoothened signaling pathway involved in dorsal/ventral neural tube patterning	IEA
GO:0061055	Process	Myotome development	IEA
GO:0065003	Process	Protein-containing complex assembly	IMP	27932497
GO:0072657	Process	Protein localization to membrane	IEA
GO:0097542	Component	Ciliary tip	TAS
GO:0097730	Component	Non-motile cilium	IEA
GO:0097730	Component	Non-motile cilium	ISS
GO:1903441	Process	Protein localization to ciliary membrane	IMP	27932497

MIM	HGNC	e!Ensembl
608151	18340	ENSG00000157796

Protein

UniProt ID

Q8NEZ3

Protein name

WD repeat-containing protein 19 (Intraflagellar transport 144 homolog)

Protein function

As component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), it is involved in cilia function and/or assembly (PubMed:20889716). Essential for functio

PDB

8BBF , 8BBG , 8FGW , 8FH3

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF15911	WD40_3	508 → 564	WD domain, G-beta repeat	Repeat

Tissue specificity

TISSUE SPECIFICITY: Some isoforms are tissue-specific. Highly expressed in the prostate. Lower expression in the cerebellum, pituitary gland, fetal lung, and pancreas. In normal prostate, expressed in both basal and luminal epithelial cells. No expression

Sequence

MKRIFSLLEKTWLGAPIQFAWQKTSGNYLAVTGADYIVKIFDRHGQKRSEINLPGNCVAM
DWDKDGDVLAVIAEKSSCIYLWDANTNKTSQLDNGMRDQMSFLLWSKVGSFLAVGTVKGN
LLIYNHQTSRKIPVLGKHTKRITCGCWNAENLLALGGEDKMITVSNQEGDTIRQTQVRSE
PSNMQFFLMKMDDRTSAAESMISVVLGKKTLFFLNLNEPDNPADLEFQQDFGNIVCYNWY
GDGRIMIGFSCGHFVVISTHTGELGQEIFQARNHKDNLTSIAVSQTLNKVATCGDNCIKI
QDLVDLKDMYVILNLDEENKGLGTLSWTDDGQLLALSTQRGSLHVFLTKLPILGDACSTR
IAYLTSLLEVTVANPVEGELPITVSVDVEPNFVAVGLYHLAVGMNNRAWFYVLGENAVKK
LKDMEYLGTVASICLHSDYAAALFEGKVQLHLIESEILDAQEERETRLFPAVDDKCRILC
HALTSDFLIYGTDTGVVQYFYIEDWQFVNDYRHPVSVKKIFPDPNGTRLVFIDEKSDGFV
YCPVNDATYEIPDFSPTIKGVLWENWPMDKGVFIAYDDDKVYTYVFHKDTIQGAKVILAG
STKVPFAHKPLLLYNGELTCQTQSGKVNNIYLSTHGFLSNLKDTGPDELRPMLAQNLMLK
RFSDAWEMCRILNDEAAWNELARACLHHMEVEFAIRVYRRIGNVGIVMSLEQIKGIEDYN
LLAGHLAMFTNDYNLAQDLYLASSCPIAALEMRRDLQHWDSALQLAKHLAPDQIPFISKE
YAIQLEFAGDYVNALAHYEKGITGDNKEHDEACLAGVAQMSIRMGDIRRGVNQALKHPSR
VLKRDCGAILENMKQFSEAAQLYEKGLYYDKAASVYIRSKNWAKVGDLLPHVSSPKIHLQ
YAKAKEADGRYKEAVVAYENAKQWQSVIRIYLDHLNNPEKAVNIVRETQSLDGAKMVARF
FLQLGDYGSAIQFLVMSKCNNEAFTLAQQHNKMEIYADIIGSEDTTNEDYQSIALYFEGE
KRYLQAGKFFLLCGQYSRALKHFLKCPSSEDNVAIEMAIETVGQAKDELLTNQLIDHLLG
ENDGMPKDAKYLFRLYMALKQYREAAQTAIIIAREEQSAGNYRNAHDVLFSMYAELKSQK
IKIPSEMATNLMILHSYILVKIHVKNGDHMKGARMLIRVANNISKFPSHIVPILTSTVIE
CHRAGLKNSAFSFAAMLMRPEYRSKIDAKYKKKIEGMVRRPDISEIEEATTPCPFCKFLL
PECELLCPGCKNSIPYCIATGRHMLKDDWTVCPHCDFPALYSELKIMLNTESTCPMCSER
LNAAQLKKISDCTQYLRTEEEL

Sequence length

1342

Interactions

View interactions

	Reactome
			Hedgehog 'off' state Intraflagellar transport

Show/Hide Causal Diseases (9)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Asphyxiating Thoracic Dystrophy	Asphyxiating thoracic dystrophy 5	rs387906980, rs1577822861, rs1327583103, rs387906982	N/A
Connective Tissue Disease	Connective tissue disorder	rs587777352, rs387906980	N/A
Cranioectodermal Dysplasia	cranioectodermal dysplasia 4	rs387906980, rs751290509, rs79436363, rs387906981	N/A
Jeune Thoracic Dystrophy	jeune thoracic dystrophy	rs745603321, rs747165335, rs1553905326, rs748656635, rs377160857, rs1215108056, rs587777352, rs772599282, rs1191056931	N/A
Nephronophthisis	nephronophthisis 13	rs786205114, rs587777350, rs587777351, rs387906983, rs587777352	N/A
retinal dystrophy	Retinal dystrophy	rs751290509	N/A
Senior-Loken Syndrome	senior-loken syndrome 8	rs587777348, rs786204852, rs374400438, rs886039814, rs387906980, rs587777351, rs886041912, rs748174246, rs79436363, rs587777352	N/A
Leber Congenital Amaurosis	leber congenital amaurosis	rs79436363	N/A
renal dysplasia and retinal aplasia	Renal dysplasia and retinal aplasia	rs387906980	N/A

Show/Hide Unknown Diseases (5)

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.
Bardet-Biedl Syndrome	bardet-biedl syndrome	N/A	N/A	ClinVar
craniosynostosis syndrome	Craniosynostosis syndrome	N/A	N/A	ClinVar
Glaucoma	Glaucoma	N/A	N/A	GWAS
Jeune Syndrome	Jeune syndrome	N/A	N/A	GenCC
Mental retardation	intellectual disability	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (27)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Caroli Disease	Associate	23559409
Ciliopathies	Associate	22019273, 23559409, 23683095, 32055034, 33875766, 34354814, 36833411, 38062428
Cranioectodermal Dysplasia	Associate	22019273, 32007091
Down Syndrome	Associate	36833411
general anxiety disorder	Associate	36344488
Genetic Diseases Inborn	Associate	36833411
Immune dysfunction with T cell inactivation due to calcium entry defect 2	Associate	38062428
Infertility Male	Associate	32323121
Iridogoniodysgenesis and skeletal anomalies	Associate	22019273
Jeune syndrome	Associate	22019273, 31935347
Kidney Diseases	Associate	22019273
Muscular dystrophy congenital merosin negative	Associate	36833411
Myopathies Nemaline	Associate	36833218
Myotonia with Skeletal Abnormalities and Mental Retardation	Associate	38062428
Nephronophthisis familial juvenile	Associate	22019273, 38589766
Night Blindness	Associate	36833218
Nonsyndromic Deafness	Associate	32323121
Obsessive Compulsive Disorder	Associate	36344488
Pancytopenia	Associate	38589766
Pathological Conditions Anatomical	Associate	36833411
Renal Insufficiency	Associate	22019273
Retinitis Pigmentosa	Associate	23683095, 33946315
Senior Loken Syndrome	Associate	23683095
Short Rib Polydactyly Syndrome	Associate	38062428
Stargardt Disease	Associate	32055034, 36833218, 36833411
Stargardt disease 3	Associate	36833218
T Lymphocytopenia Idiopathic CD4 Positive	Associate	38589766

WDR19 (WD repeat domain 19)