Gene Gene information from NCBI Gene database.
Entrez ID 4867
Gene name Nephrocystin 1
Gene symbol NPHP1
Synonyms (NCBI Gene)
JBTS4NPH1SLSN1
Chromosome 2
Chromosome location 2q13
Summary 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
SNPs SNP information provided by dbSNP.
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
miRNA miRNA information provided by mirtarbase database.
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
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
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
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
607100 7905 ENSG00000144061
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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
VIEKKPDGWWIAKDAKGNEGLVPR
TYLEPYSEEEEGQESSEEGSEEDVEAVDETADGAEV
KQRTDPHWSAVQKAISEAGIFCLVNHVSFCYLIVLMRNRMETVEDTNGSETGFRAWNVQS
RGRIFLVSKPVLQINTVDVLTTMGAIPAGFRPSTLSQLLEEGNQFRANYFLQPELMPSQL
AFRDLMWDATEGTIRSRPSRISLILTLWSCKMIPLPGMSIQVLSRHVRLCLFDGNKVLSN
IHTVRATWQPKKPKTWTFSPQVTRILPCLLDGDCFIRSNSASPDLGILFELGISYIRNST
GERGELSCGWVFLKLFDASGVPIPAKTYELFLNGGTPYEKGIEVDPSISRRAHGSVFYQI
MTMRRQPQLLVKLRSLNRRSRNVLSLLPETLIGNMCSIHLLIFYRQILGDVLLKDRMSLQ
STDLISHPMLATFPMLLEQPDVMDALRSSWAGKESTLKRSEKRDKEFLKSTFLLVYHDCV
LPLLHSTRLPPFRWAEEETETARWKVITDFLKQNQENQGALQALLSPDGVHEPFDLSEQT
YDFLGEMRKNAV
Sequence length 732
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Anchoring of the basal body to the plasma membrane
Associated diseases Disease associations from ClinVar categorized as Causal (Pathogenic/Likely Pathogenic) or Unknown.
1437
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Clear cell carcinoma of kidney Pathogenic rs121907899 RCV005887255
Congenital anomaly of kidney and urinary tract Pathogenic rs754137355 RCV001849622
Joubert syndrome and related disorders Likely pathogenic; Pathogenic rs752708835, rs564605452, rs376974221, rs1017750255 RCV002282819
RCV003155856
RCV003492029
RCV003155299
Joubert syndrome with renal defect Pathogenic; Likely pathogenic rs547352656, rs2104483923, rs376492641, rs1410236296, rs772720024, rs773781058, rs745806504, rs752708835, rs1233478832, rs121907899, rs367600757, rs1388373598, rs564605452, rs766524637, rs376974221
View all (43 more)
RCV001332330
RCV003469752
RCV003469780
RCV003469679
RCV004571682
RCV002492327
RCV002497908
RCV003471306
RCV003466796
RCV003466797
RCV003465966
RCV005021662
RCV003466028
RCV003463749
RCV002494861
RCV003471527
RCV003471528
RCV003471529
RCV003471530
RCV003471531
RCV003471532
RCV003471533
RCV003471534
RCV003463183
RCV003463184
RCV003471535
RCV003471536
RCV003471537
RCV003471538
RCV003471539
RCV003471540
RCV003471541
RCV003476576
RCV003463185
RCV003471542
RCV003471543
RCV003471544
RCV003463186
RCV003471545
RCV003463187
RCV003471546
RCV003471547
RCV003471548
RCV003471549
RCV003476577
RCV005014767
RCV005014801
RCV004574367
RCV004574368
RCV004574369
RCV004574370
RCV004574371
RCV002507229
RCV002493328
RCV003465664
RCV001260993
RCV002497439
RCV002505566
RCV004566944
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession
Acute myeloid leukemia Benign; Likely benign rs113450177 RCV005895106
Bardet-Biedl syndrome 1 Uncertain significance rs373953762 RCV003229050
Cervical cancer Benign; Likely benign rs113450177 RCV005895107
Focal segmental glomerulosclerosis Benign rs33958626 RCV002294035
Associations from Text MiningDisease associations identified through Pubtator
Disease Name Relationship Type References
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