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.	4867
Gene name Gene Name - the full gene name approved by the HGNC.	Nephrocystin 1
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	NPHP1
Synonyms (NCBI Gene) Gene synonyms aliases	JBTS4, NPH1, SLSN1
Chromosome Chromosome number	2
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	2q13
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein with src homology domain 3 (SH3) patterns. This protein interacts with Crk-associated substrate, and it appears to function in the control of cell division, as well as in cell-cell and cell-matrix adhesion signaling, likely as

Show/Hide all(22)

SNP ID	Visualize variation	Clinical significance	Consequence
rs114250691	A>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs121907898	A>C,T	Pathogenic	Stop gained, coding sequence variant, missense variant
rs121907899	C>A,T	Pathogenic	Coding sequence variant, missense variant
rs140446520	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance, likely-benign	Coding sequence variant, intron variant, missense variant
rs140469160	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs141763330	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant
rs144217506	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs144850331	C>G,T	Conflicting-interpretations-of-pathogenicity	3 prime UTR variant, synonymous variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant
rs371112962	T>C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant
rs373915635	G>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs376974221	C>T	Pathogenic	Intron variant, splice donor variant
rs398123285	->G	Pathogenic	Coding sequence variant, frameshift variant
rs747861275	C>-	Pathogenic	Splice donor variant, genic downstream transcript variant
rs760619900	C>G	Likely-pathogenic	Genic downstream transcript variant, coding sequence variant, 3 prime UTR variant, downstream transcript variant, missense variant
rs763004817	T>C	Conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant
rs765263671	G>A	Pathogenic	Coding sequence variant, stop gained
rs766524637	T>-,TT	Pathogenic	Frameshift variant, coding sequence variant
rs779032904	A>-	Conflicting-interpretations-of-pathogenicity	Intron variant, genic downstream transcript variant
rs1017750255	A>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant
rs1233478832	C>A	Pathogenic	Splice donor variant, genic downstream transcript variant
rs1349732291	C>A	Pathogenic	Coding sequence variant, stop gained
rs1553484094	TC>-	Pathogenic	Frameshift variant, coding sequence variant, genic downstream transcript variant

Show/Hide all(106)

miRTarBase ID	miRNA	Experiments	Reference
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT679316	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT679315	hsa-miR-6131	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT679314	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT679313	hsa-miR-6848-3p	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670609	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT670605	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT679316	hsa-miR-3663-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT679315	hsa-miR-6131	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT679314	hsa-miR-6843-3p	HITS-CLIP	23824327
MIRT679313	hsa-miR-6848-3p	HITS-CLIP	23824327
MIRT670620	hsa-miR-125a-3p	HITS-CLIP	23824327
MIRT670619	hsa-miR-764	HITS-CLIP	23824327
MIRT670618	hsa-miR-3934-5p	HITS-CLIP	23824327
MIRT670617	hsa-miR-1224-3p	HITS-CLIP	23824327
MIRT670616	hsa-miR-1234-3p	HITS-CLIP	23824327
MIRT670615	hsa-miR-7107-5p	HITS-CLIP	23824327
MIRT670614	hsa-miR-371b-5p	HITS-CLIP	23824327
MIRT670613	hsa-miR-373-5p	HITS-CLIP	23824327
MIRT670612	hsa-miR-616-5p	HITS-CLIP	23824327
MIRT670611	hsa-miR-371a-5p	HITS-CLIP	23824327
MIRT670610	hsa-miR-372-5p	HITS-CLIP	23824327
MIRT670609	hsa-miR-150-5p	HITS-CLIP	23824327
MIRT670608	hsa-miR-3653-5p	HITS-CLIP	23824327
MIRT670607	hsa-miR-6790-3p	HITS-CLIP	23824327
MIRT670606	hsa-miR-6821-3p	HITS-CLIP	23824327
MIRT670605	hsa-miR-6778-3p	HITS-CLIP	23824327
MIRT670604	hsa-miR-378a-5p	HITS-CLIP	23824327
MIRT670603	hsa-miR-640	HITS-CLIP	23824327
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq
MIRT2284161	hsa-miR-106a	CLIP-seq
MIRT2284162	hsa-miR-106b	CLIP-seq
MIRT2284163	hsa-miR-17	CLIP-seq
MIRT2284164	hsa-miR-20a	CLIP-seq
MIRT2284165	hsa-miR-20b	CLIP-seq
MIRT2284166	hsa-miR-3609	CLIP-seq
MIRT2284167	hsa-miR-382	CLIP-seq
MIRT2284168	hsa-miR-4645-3p	CLIP-seq
MIRT2284169	hsa-miR-4796-3p	CLIP-seq
MIRT2284170	hsa-miR-519d	CLIP-seq
MIRT2284171	hsa-miR-542-3p	CLIP-seq
MIRT2284172	hsa-miR-548ah	CLIP-seq
MIRT2284173	hsa-miR-93	CLIP-seq
MIRT2391695	hsa-miR-568	CLIP-seq
MIRT2391696	hsa-miR-944	CLIP-seq
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq
MIRT1190697	hsa-miR-3137	CLIP-seq
MIRT1190698	hsa-miR-3686	CLIP-seq
MIRT1190699	hsa-miR-4307	CLIP-seq
MIRT1190700	hsa-miR-4446-5p	CLIP-seq
MIRT1190701	hsa-miR-4778-5p	CLIP-seq

Show/Hide all(28)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005198	Function	Structural molecule activity	NAS	12006559
GO:0005515	Function	Protein binding	IPI	12244321, 12872122, 15661758, 16374509, 18633336, 20664800, 20856870, 21357692, 21565611, 21633164, 23532844, 25825872, 26638075, 27173435, 29959317, 33961781
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005911	Component	Cell-cell junction	IDA	21565611
GO:0005912	Component	Adherens junction	IEA
GO:0005923	Component	Bicellular tight junction	IEA
GO:0005929	Component	Cilium	IBA
GO:0005929	Component	Cilium	IEA
GO:0007165	Process	Signal transduction	NAS	12244321
GO:0007283	Process	Spermatogenesis	IEA
GO:0007632	Process	Visual behavior	NAS	12205563
GO:0016020	Component	Membrane	NAS	10665934
GO:0030030	Process	Cell projection organization	IEA
GO:0030030	Process	Cell projection organization	ISS
GO:0030036	Process	Actin cytoskeleton organization	NAS	12006559
GO:0030154	Process	Cell differentiation	IEA
GO:0031514	Component	Motile cilium	IDA	16885411
GO:0032391	Component	Photoreceptor connecting cilium	ISS
GO:0042995	Component	Cell projection	IEA
GO:0048515	Process	Spermatid differentiation	ISS
GO:0060041	Process	Retina development in camera-type eye	ISS
GO:0070161	Component	Anchoring junction	IEA
GO:0090251	Process	Protein localization involved in establishment of planar polarity	IBA
GO:0098609	Process	Cell-cell adhesion	NAS	12006559
GO:1903348	Process	Positive regulation of bicellular tight junction assembly	IMP	19755384

MIM	HGNC	e!Ensembl
607100	7905	ENSG00000144061

Protein

UniProt ID

O15259

Protein name

Nephrocystin-1 (Juvenile nephronophthisis 1 protein)

Protein function

Together with BCAR1 it may play a role in the control of epithelial cell polarity (By similarity). Involved in the organization of apical junctions in kidney cells together with NPHP4 and RPGRIP1L/NPHP8 (By similarity). Does not seem to be stric

PDB

1S1N , 6O1Q

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00018	SH3_1	158 → 204	SH3 domain	Domain

Tissue specificity

TISSUE SPECIFICITY: Widespread expression, with highest levels in pituitary gland, spinal cord, thyroid gland, testis, skeletal muscle, lymph node and trachea. Weakly expressed in heart, kidney and pancreas. Expressed in nasal epithelial cells (at protein

Sequence

MLARRQRDPLQALRRRNQELKQQVDSLLSESQLKEALEPNKRQHIYQRCIQLKQAIDENK
NALQKLSKADESAPVANYNQRKEEEHTLLDKLTQQLQGLAVTISRENITEVGAPTEEEEE
SESEDSEDSGGEEEDAEEEEEEKEENESHKWSTGEEYIAVGDFTAQQVGDLTFKKGEILL
VIEKKPDGWWIAKDAKGNEGLVPRTYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV
KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQS
RGRIFLVSKPVLQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQL
AFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSN
IHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNST
GERGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQI
MTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQ
STDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCV
LPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQT
YDFLGEMRKNAV

Sequence length

732

Interactions

View interactions

	Reactome
			Anchoring of the basal body to the plasma membrane

Show/Hide Causal Diseases (4)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Joubert Syndrome	Joubert syndrome and related disorders	rs1017750255, rs376974221	N/A
Joubert Syndrome With Renal Defect	joubert syndrome with renal defect	rs1233478832, rs766524637, rs1017750255, rs376974221, rs1311042980, rs121907899, rs753517219, rs398123285, rs765263671	N/A
Nephronophthisis	nephronophthisis 1, nephronophthisis	rs766524637, rs1017750255, rs121907898, rs376974221, rs1679148969, rs121907899, rs1311042980, rs1553484094, rs747861275, rs1682584195, rs398123285, rs765263671, rs753517219, rs1233478832, rs1349732291	N/A
retinal dystrophy	Retinal dystrophy	rs121907899	N/A

Show/Hide Unknown Diseases (8)

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	GenCC
Cerebellar vermis agenesis	familial aplasia of the vermis	N/A	N/A	ClinVar
focal segmental glomerulosclerosis	Focal segmental glomerulosclerosis	N/A	N/A	ClinVar
Leber Congenital Amaurosis	leber congenital amaurosis	N/A	N/A	ClinVar
Mental Retardation, X-Linked	Intellectual disability, X-linked 102	N/A	N/A	ClinVar
Neuroticism	Neuroticism	N/A	N/A	GWAS
renal dysplasia and retinal aplasia	Renal dysplasia and retinal aplasia	N/A	N/A	ClinVar
Senior-Loken Syndrome	Senior-Loken syndrome	N/A	N/A	GenCC

Show/Hide Text Mining Associations (44)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Acute Kidney Injury	Associate	40725491
Agenesis of Cerebellar Vermis	Associate	15138899, 15467982, 15786477, 16155189, 16900087, 17960139, 18950740, 22982934, 28347285, 28596487, 28667057, 30055837, 37131188, 37296294, 37735380
Alzheimer Disease	Associate	22710270
Apraxia oculomotor Cogan type	Associate	37131188
Arrest of spermatogenesis	Associate	26198798
Autism Spectrum Disorder	Associate	28254236
Brain Stem Neoplasms	Associate	17160906
Capillary Malformation Arteriovenous Malformation	Associate	16900087
Cholestasis	Associate	36227438
Ciliopathies	Associate	21068128, 21357692, 21866095, 22982934, 27491411, 28596487, 29146700, 35764379, 36227438
Cone Rod Dystrophies	Associate	29555955
Congenital Abnormalities	Associate	28347285
Disease	Associate	37296294
Glycosuria Renal	Associate	10712196
Hydatidiform Mole	Associate	16900087
Hydrocephalus Normal Pressure	Associate	11168925
Infertility Male	Associate	26198798
Intellectual Disability	Associate	28254236
Joubert syndrome 4	Associate	37131188
Kidney Diseases	Associate	16155189, 27004562, 36227438, 37203120
Kidney Diseases Cystic	Associate	22701722, 26198798, 35676033
Kidney Failure Chronic	Associate	11168925, 21258817, 26198798, 29146700, 29654215, 31096956, 32306954, 35676033, 37296294
Leukemia Hairy Cell	Associate	32132867
Liver Failure	Associate	28254236
Macular Degeneration	Associate	20981449
Male Infertility with Large Headed Multiflagellar Polyploid Spermatozoa	Associate	26662397
Medullary cystic kidney disease 1	Associate	12234310
Multiple Organ Failure	Associate	29146700
Muscle Hypotonia	Associate	16900087
Neoplasms	Associate	37296294
Neoplastic Syndromes Hereditary	Associate	31922211
Nephronophthisis 2	Associate	21866095, 25851290, 37203120
Nephronophthisis 3	Associate	31922211
Nephronophthisis familial juvenile	Associate	10712196, 11168925, 15138899, 15467982, 15786477, 16155189, 16900087, 17160906, 17617513, 18076122, 21258817, 21357692, 22701722, 22982934, 25851290 View all (15 more)
Nephronophthisis familial juvenile	Stimulate	21866095
Nephrosis congenital	Associate	27004562
Nervous System Malformations	Associate	16900087
Neurologic Manifestations	Associate	16900087
Renal Insufficiency	Associate	16900087, 36227438, 37203120
Renal Insufficiency Chronic	Associate	37203120
Retinitis Pigmentosa	Associate	40725491
Senior Loken Syndrome	Associate	37296294, 40725491
Signs and Symptoms	Associate	16900087
Vision Disorders	Associate	40725491

NPHP1 (nephrocystin 1)