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.	261734
Gene name Gene Name - the full gene name approved by the HGNC.	Nephrocystin 4
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NPHP4
Synonyms (NCBI Gene) Gene synonyms aliases	POC10, SLSN4
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p36.31
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are ass

Show/Hide all(65)

SNP ID	Visualize variation	Clinical significance	Consequence
rs17472401	G>A	Benign, conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, non coding transcript variant
rs28940891	A>G	Pathogenic	Genic downstream transcript variant, coding sequence variant, non coding transcript variant, downstream transcript variant, missense variant
rs35575973	C>T	Uncertain-significance, conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, non coding transcript variant, intron variant, downstream transcript variant, synonymous variant, genic downstream transcript variant
rs35959882	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant, non coding transcript variant
rs112206586	T>A,G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, missense variant, coding sequence variant
rs115272639	C>T	Conflicting-interpretations-of-pathogenicity	5 prime UTR variant, non coding transcript variant, synonymous variant, coding sequence variant
rs116606479	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, downstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs117898549	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	5 prime UTR variant, non coding transcript variant, missense variant, coding sequence variant
rs137852918	C>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs137852919	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs137852920	G>A,T	Likely-pathogenic, pathogenic	Stop gained, non coding transcript variant, synonymous variant, coding sequence variant
rs137852922	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs137852923	G>A	Pathogenic	Stop gained, non coding transcript variant, coding sequence variant
rs139767853	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance, benign	Genic downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant
rs146948888	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant
rs183885357	C>T	Conflicting-interpretations-of-pathogenicity, benign	Downstream transcript variant, non coding transcript variant, missense variant, coding sequence variant, genic downstream transcript variant
rs191913664	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, intron variant, coding sequence variant, non coding transcript variant
rs199557439	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, coding sequence variant, synonymous variant, non coding transcript variant
rs199628481	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant, coding sequence variant, synonymous variant, non coding transcript variant
rs199925943	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, intron variant, synonymous variant, genic downstream transcript variant
rs200104274	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant
rs200166175	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs200952409	G>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs201065230	A>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant, genic upstream transcript variant, non coding transcript variant, missense variant, coding sequence variant, 5 prime UTR variant
rs201069164	G>A	Conflicting-interpretations-of-pathogenicity	Upstream transcript variant, synonymous variant, intron variant, non coding transcript variant, genic upstream transcript variant, coding sequence variant, 5 prime UTR variant
rs201074950	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, downstream transcript variant, missense variant, coding sequence variant, genic downstream transcript variant
rs201090359	G>A,C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, non coding transcript variant, intron variant, missense variant, coding sequence variant
rs201192584	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs201488441	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, 5 prime UTR variant, synonymous variant, non coding transcript variant
rs201903713	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs368961102	C>T	Conflicting-interpretations-of-pathogenicity	Intron variant, genic upstream transcript variant
rs370210428	G>A	Pathogenic	Intron variant, genic upstream transcript variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant, stop gained
rs370899989	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Intron variant
rs372430727	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs373182062	G>A,C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs373369949	G>A,T	Likely-pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant, intron variant
rs374003717	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs374141736	C>G,T	Pathogenic	Splice donor variant
rs374354239	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, genic downstream transcript variant, coding sequence variant, intron variant
rs374690894	C>T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, missense variant, non coding transcript variant
rs375493384	C>G,T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant
rs398124289	->GAGCG	Pathogenic	Frameshift variant, non coding transcript variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant
rs528547815	G>A,T	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, genic downstream transcript variant, non coding transcript variant
rs545943420	G>A	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, genic upstream transcript variant, coding sequence variant, synonymous variant, 5 prime UTR variant
rs547495754	G>A	Uncertain-significance, pathogenic	Missense variant, coding sequence variant, non coding transcript variant
rs569364202	G>A	Pathogenic	Non coding transcript variant, downstream transcript variant, genic downstream transcript variant, missense variant, coding sequence variant
rs570380438	A>T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs747699128	GAGG>-	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant
rs754862360	G>-,GG	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, intron variant, 5 prime UTR variant
rs756449736	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, intron variant, coding sequence variant, non coding transcript variant
rs758275952	G>A	Pathogenic	Stop gained, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs758757125	G>A	Conflicting-interpretations-of-pathogenicity	Downstream transcript variant, synonymous variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant
rs762371581	TAGA>-	Pathogenic	Genic downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant
rs762709199	G>A	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant, genic downstream transcript variant, downstream transcript variant
rs775612958	G>A	Likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, genic downstream transcript variant, stop gained
rs1025515771	G>A	Pathogenic	Coding sequence variant, non coding transcript variant, stop gained
rs1210874691	C>A	Pathogenic	Non coding transcript variant, coding sequence variant, stop gained, 5 prime UTR variant
rs1278089386	A>-	Pathogenic	Genic downstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs1368105372	TGAG>-	Likely-pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant
rs1487910110	C>T	Likely-pathogenic	Non coding transcript variant, coding sequence variant, missense variant
rs1553178047	GTT>CCACG	Likely-pathogenic	Non coding transcript variant, frameshift variant, coding sequence variant
rs1553200990	TCAA>-	Pathogenic	Intron variant, 5 prime UTR variant, upstream transcript variant, non coding transcript variant, genic upstream transcript variant, frameshift variant, coding sequence variant
rs1557588167	G>-	Pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant, non coding transcript variant
rs1557768696	->GG	Likely-pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, 5 prime UTR variant
rs1570504754	->GG	Likely-pathogenic	Frameshift variant, non coding transcript variant, 5 prime UTR variant, coding sequence variant

Show/Hide all(24)

miRTarBase ID	miRNA	Experiments
MIRT1190809	hsa-miR-15a	CLIP-seq
MIRT1190810	hsa-miR-15b	CLIP-seq
MIRT1190811	hsa-miR-16	CLIP-seq
MIRT1190812	hsa-miR-195	CLIP-seq
MIRT1190813	hsa-miR-214	CLIP-seq
MIRT1190814	hsa-miR-320e	CLIP-seq
MIRT1190815	hsa-miR-3619-5p	CLIP-seq
MIRT1190816	hsa-miR-370	CLIP-seq
MIRT1190817	hsa-miR-424	CLIP-seq
MIRT1190818	hsa-miR-4291	CLIP-seq
MIRT1190819	hsa-miR-4455	CLIP-seq
MIRT1190820	hsa-miR-4650-5p	CLIP-seq
MIRT1190821	hsa-miR-4731-5p	CLIP-seq
MIRT1190822	hsa-miR-497	CLIP-seq
MIRT1190823	hsa-miR-609	CLIP-seq
MIRT1190824	hsa-miR-646	CLIP-seq
MIRT1190825	hsa-miR-761	CLIP-seq
MIRT1190826	hsa-miR-922	CLIP-seq
MIRT2055230	hsa-miR-1205	CLIP-seq
MIRT2055231	hsa-miR-1909	CLIP-seq
MIRT2055232	hsa-miR-4436b-3p	CLIP-seq
MIRT2055233	hsa-miR-4459	CLIP-seq
MIRT2055234	hsa-miR-4722-5p	CLIP-seq
MIRT2055235	hsa-miR-4779	CLIP-seq

Show/Hide all(41)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005198	Function	Structural molecule activity	NAS	12006559
GO:0005515	Function	Protein binding	IPI	12244321, 15661758, 16339905, 17558407, 20664800, 21224891, 21357692, 21565611, 22654112, 22863007, 26638075, 26644512, 27173435, 29959317, 33961781
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005813	Component	Centrosome	IDA	21399614
GO:0005813	Component	Centrosome	IEA
GO:0005814	Component	Centriole	IEA
GO:0005829	Component	Cytosol	IDA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005911	Component	Cell-cell junction	IDA	21565611
GO:0005923	Component	Bicellular tight junction	IEA
GO:0005929	Component	Cilium	IEA
GO:0007165	Process	Signal transduction	NAS	12244321
GO:0007632	Process	Visual behavior	NAS	12205563
GO:0016604	Component	Nuclear body	IDA
GO:0030036	Process	Actin cytoskeleton organization	NAS	12006559
GO:0030317	Process	Flagellated sperm motility	IEA
GO:0032391	Component	Photoreceptor connecting cilium	IEA
GO:0035845	Process	Photoreceptor cell outer segment organization	IEA
GO:0035869	Component	Ciliary transition zone	IBA
GO:0035869	Component	Ciliary transition zone	IEA
GO:0036064	Component	Ciliary basal body	IBA
GO:0036064	Component	Ciliary basal body	IEA
GO:0042995	Component	Cell projection	IEA
GO:0045494	Process	Photoreceptor cell maintenance	IEA
GO:0060041	Process	Retina development in camera-type eye	IEA
GO:0070161	Component	Anchoring junction	IEA
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IBA
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IDA	22654112
GO:0090090	Process	Negative regulation of canonical Wnt signaling pathway	IEA
GO:0097470	Component	Ribbon synapse	IEA
GO:0097546	Component	Ciliary base	IBA
GO:0097546	Component	Ciliary base	IEA
GO:0097730	Component	Non-motile cilium	IBA
GO:0097730	Component	Non-motile cilium	IEA
GO:0098609	Process	Cell-cell adhesion	NAS	12006559
GO:0120206	Component	Photoreceptor distal connecting cilium	IEA
GO:1903348	Process	Positive regulation of bicellular tight junction assembly	IMP	19755384
GO:1904491	Process	Protein localization to ciliary transition zone	IBA

MIM	HGNC	e!Ensembl
607215	19104	ENSG00000131697

Protein

UniProt ID

O75161

Protein name

Nephrocystin-4 (Nephroretinin)

Protein function

Involved in the organization of apical junctions; the function is proposed to implicate a NPHP1-4-8 module (PubMed:19755384, PubMed:21565611). Does not seem to be strictly required for ciliogenesis (PubMed:21565611). Required for building functi

Family and domains

Tissue specificity

TISSUE SPECIFICITY: Expressed in kidney, skeletal muscle, heart and liver, and to a lesser extent in brain and lung. {ECO:0000269|PubMed:12244321}.

Sequence

MNDWHRIFTQNVLVPPHPQRARQPWKESTAFQCVLKWLDGPVIRQGVLEVLSEVECHLRV
SFFDVTYRHFFGRTWKTTVKPTKRPPSRIVFNEPLYFHTSLNHPHIVAVVEVVAEGKKRD
GSLQTLSCGFGILRIFSNQPDSPISASQDKRLRLYHGTPRALLHPLLQDPAEQNRHMTLI
ENCSLQYTLKPHPALEPAFHLLPENLLVSGLQQIPGLLPAHGESGDALRKPRLQKPITGH
LDDLFFTLYPSLEKFEEELLELHVQDHFQEGCGPLDGGALEILERRLRVGVHNGLGFVQR
PQVVVLVPEMDVALTRSASFSRKVVSSSKTSSGSQALVLRSRLRLPEMVGHPAFAVIFQL
EYVFSSPAGVDGNAASVTSLSNLACMHMVRWAVWNPLLEADSGRVTLPLQGGIQPNPSHC
LVYKVPSASMSSEEVKQVESGTLRFQFSLGSEEHLDAPTEPVSGPKVERRPSRKPPTSPS
SPPAPVPRVLAAPQNSPVGPGLSISQLAASPRSPTQHCLARPTSQLPHGSQASPAQAQEF
PLEAGISHLEADLSQTSLVLETSIAEQLQELPFTPLHAPIVVGTQTRSSAGQPSRASMVL
LQSSGFPEILDANKQPAEAVSATEPVTFNPQKEESDCLQSNEMVLQFLAFSRVAQDCRGT
SWPKTVYFTFQFYRFPPATTPRLQLVQLDEAGQPSSGALTHILVPVSRDGTFDAGSPGFQ
LRYMVGPGFLKPGERRCFARYLAVQTLQIDVWDGDSLLLIGSAAVQMKHLLRQGRPAVQA
SHELEVVATEYEQDNMVVSGDMLGFGRVKPIGVHSVVKGRLHLTLANVGHPCEQKVRGCS
TLPPSRSRVISNDGASRFSGGSLLTTGSSRRKHVVQAQKLADVDSELAAMLLTHARQGKG
PQDVSRESDATRRRKLERMRSVRLQEAGGDLGRRGTSVLAQQSVRTQHLRDLQVIAAYRE
RTKAESIASLLSLAITTEHTLHATLGVAEFFEFVLKNPHNTQHTVTVEIDNPELSVIVDS
QEWRDFKGAAGLHTPVEEDMFHLRGSLAPQLYLRPHETAHVPFKFQSFSAGQLAMVQASP
GLSNEKGMDAVSPWKSSAVPTKHAKVLFRASGGKPIAVLCLTVELQPHVVDQVFRFYHPE
LSFLKKAIRLPPWHTFPGAPVGMLGEDPPVHVRCSDPNVICETQNVGPGEPRDIFLKVAS
GPSPEIKDFFVIIYSDRWLATPTQTWQVYLHSLQRVDVSCVAGQLTRLSLVLRGTQTVRK
VRAFTSHPQELKTDPKGVFVLPPRGVQDLHVGVRPLRAGSRFVHLNLVDVDCHQLVASWL
VCLCCRQPLISKAFEIMLAAGEGKGVNKRITYTNPYPSRRTFHLHSDHPELLRFREDSFQ
VGGGETYTIGLQFAPSQRVGEEEILIYINDHEDKNEEAFCVKVIYQ

Sequence length

1426

Interactions

View interactions

	Reactome
			Signaling by Hippo Anchoring of the basal body to the plasma membrane

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
Nephronophthisis	nephronophthisis 4, nephronophthisis	rs28940891, rs1553200990, rs775612958, rs1278089386, rs1553178047, rs370210428, rs1570504754, rs754862360, rs137852922, rs137852918, rs1557580413, rs1652115764, rs137852923, rs1368105372, rs137852919 View all (7 more)	N/A
retinal dystrophy	Retinal dystrophy	rs370210428, rs1643875847, rs756111113	N/A
Senior-Loken Syndrome	senior-loken syndrome 4	rs137852922, rs370210428, rs137852923	N/A

Show/Hide Unknown Diseases (11)

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.
Alzheimer disease	Alzheimer's disease or family history of Alzheimer's disease	N/A	N/A	GWAS
Bardet-Biedl Syndrome	bardet-biedl syndrome	N/A	N/A	ClinVar
Cholestasis	cholestasis	N/A	N/A	ClinVar
Congenital anomalies of kidney and urinary tract	Congenital anomaly of kidney and urinary tract	N/A	N/A	ClinVar
Diabetes	Chronic kidney disease in type 2 diabetes	N/A	N/A	GWAS
focal segmental glomerulosclerosis	Focal segmental glomerulosclerosis	N/A	N/A	ClinVar
Hemolytic Uremic Syndrome	Atypical hemolytic-uremic syndrome	N/A	N/A	ClinVar
Leber Congenital Amaurosis	leber congenital amaurosis	N/A	N/A	ClinVar
Lynch syndrome	Lynch syndrome 1	N/A	N/A	ClinVar
Optic Atrophy	optic atrophy	N/A	N/A	ClinVar
renal dysplasia and retinal aplasia	Renal dysplasia and retinal aplasia	N/A	N/A	ClinVar

Show/Hide Text Mining Associations (19)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Ciliopathies	Associate	21068128, 21357692
Conotruncal cardiac defects	Associate	36789878
Deafness Cataract Retinitis Pigmentosa And Sperm Abnormalities	Associate	37831349
Enuresis	Associate	25818963
Fibrosis	Associate	24516231
Glomerulosclerosis Focal Segmental	Associate	34435324
Hypertensive Retinopathy	Associate	40725491
Infertility Male	Associate	37831349
Kidney Diseases	Associate	40725491
Kidney Failure Chronic	Associate	25818963
Kidney Neoplasms	Associate	24516231
Lung Neoplasms	Associate	22797725
Nephronophthisis 4	Associate	12205563
Nephronophthisis familial juvenile	Associate	11920287, 12205563, 15776426, 17617513, 18076122, 21357692, 25818963, 31810733
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	36316773
Renal Insufficiency	Associate	31810733
Renal Insufficiency Chronic	Associate	25818963
Retinitis Pigmentosa	Associate	11920287, 12205563
Senior Loken Syndrome	Associate	11920287, 40725491

NPHP4 (nephrocystin 4)