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| TissGeneSummary for NPHP1 |
 Gene summary |
| Basic gene information | Gene symbol | NPHP1 |
| Gene name | nephronophthisis 1 (juvenile) | |
| Synonyms | JBTS4|NPH1|SLSN1 | |
| Cytomap | UCSC genome browser: 2q13 | |
| Type of gene | protein-coding | |
| RefGenes | NM_000272.3, NM_001128178.1,NM_001128179.1,NM_207181.2, | |
| Description | juvenile nephronophthisis 1 proteinnephrocystin 1nephrocystin-1 | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 607100 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000144061 | ||
| HPRD : 02019 | ||
| HPRD : 09524 | ||
| Vega : OTTHUMG00000131195 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_NPHP1 | |
| BioGPS: 4867 | ||
| Pathway | NCI Pathway Interaction Database: NPHP1 | |
| KEGG: NPHP1 | ||
| REACTOME: NPHP1 | ||
| Pathway Commons: NPHP1 | ||
| Context | iHOP: NPHP1 | |
| ligand binding site mutation search in PubMed: NPHP1 | ||
| UCL Cancer Institute: NPHP1 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
| Reference showing the relevant tissue of NPHP1 | ||
| Description by TissGene annotations | ||
| * Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID |
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| TissGeneExp for NPHP1 |
| Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
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| Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
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| Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| KICH | 0.056645481 | 2.491765481 | -2.43512 | 3.54E-13 | 4.62E-12 |
| LUSC | 0.894198501 | 2.177351442 | -1.283152941 | 3.51E-12 | 1.54E-11 |
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| TissGene-miRNA for NPHP1 |
| Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
| Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for NPHP1 |
| TissGeneSNV for NPHP1 |
| nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
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| Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.R347* | SKCM | 3 |
| p.G154S | STAD | 2 |
| p.F714L | LUAD | 1 |
| p.C262S | SKCM | 1 |
| p.H712Y | SARC | 1 |
| p.P518S | SKCM | 1 |
| p.T651R | BLCA | 1 |
| p.L272I | KIRC | 1 |
| p.G216D | SKCM | 1 |
| p.Q22X | COAD | 1 |
| p.F614L | MESO | 1 |
| p.G482D | SKCM | 1 |
| p.L10V | LUAD | 1 |
| p.S113F | SKCM | 1 |
| p.Y294H | COAD | 1 |
| p.F715L | LUAD | 1 |
| p.P505L | SKCM | 1 |
| p.R277* | GBM | 1 |
| p.S152* | HNSC | 1 |
| p.R409C | BRCA | 1 |
| p.I304V | UCEC | 1 |
| p.K241* | PRAD | 1 |
| p.D708N | LUAD | 1 |
| p.E570K | BLCA | 1 |
| p.I273R | OV | 1 |
| p.A254V | UCEC | 1 |
| p.R294S | BLCA | 1 |
| p.S383L | SKCM | 1 |
| p.R14W | ESCA | 1 |
| p.Q442R | UCEC | 1 |
| p.P186H | KIRC | 1 |
| p.F357L | COAD | 1 |
| p.L272I | ESCA | 1 |
| p.P462S | SKCM | 1 |
| p.L88F | KIRP | 1 |
| p.L404F | SARC | 1 |
| p.L88F | SKCM | 1 |
| p.P449L | SKCM | 1 |
| p.F456L | COAD | 1 |
| p.A258V | BLCA | 1 |
| p.E679Q | CESC | 1 |
| p.S530F | UCEC | 1 |
| p.T652R | BLCA | 1 |
| p.L201R | SKCM | 1 |
| p.R478C | HNSC | 1 |
| p.D723G | UCS | 1 |
| p.E208X | READ | 1 |
| p.L511F | ACC | 1 |
| p.D659G | ESCA | 1 |
| p.E134K | LUAD | 1 |
| p.R586* | SKCM | 1 |
| p.S505X | READ | 1 |
| p.R478C | UCEC | 1 |
| p.E681Q | LUAD | 1 |
| p.A254E | LUAD | 1 |
| p.T286N | STAD | 1 |
| p.Q696K | THYM | 1 |
| p.P441T | ESCA | 1 |
| p.E85K | UCEC | 1 |
| p.V502F | LUAD | 1 |
| p.V733L | BLCA | 1 |
| p.E110G | PRAD | 1 |
| p.A362T | KIRC | 1 |
| p.R422H | SKCM | 1 |
| p.G259D | PAAD | 1 |
| p.R728K | STAD | 1 |
| p.E133X | STAD | 1 |
| p.M598I | BLCA | 1 |
| p.R301T | CESC | 1 |
| p.M393R | LUAD | 1 |
| p.R729K | STAD | 1 |
| p.S667P | LIHC | 1 |
| p.L455F | ACC | 1 |
| p.A100D | PAAD | 1 |
| p.R381C | SKCM | 1 |
| p.R42I | UCEC | 1 |
| p.R7L | HNSC | 1 |
| p.M392R | LUAD | 1 |
| p.R277Q | SKCM | 1 |
| p.V501F | LUAD | 1 |
| p.P463A | LUAD | 1 |
| p.E133* | STAD | 1 |
| p.D709N | LUAD | 1 |
| p.R478H | SKCM | 1 |
| p.E281Q | BLCA | 1 |
| p.R586Q | PRAD | 1 |
| p.P464A | LUAD | 1 |
| p.P615T | SKCM | 1 |
| p.E142D | BLCA | 1 |
| p.V168L | OV | 1 |
| p.C489Y | LGG | 1 |
| p.N278K | KIRP | 1 |
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| TissGeneCNV for NPHP1 |
| Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
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| TissGeneFusions for NPHP1 |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
| Chimerdb3.0 | ChiTaRs | NA | AW206715 | NPHP1-RAMP2 | chr2:110922073 | chr17:40914931 | |
| Chimerdb3.0 | ChiTaRs | NA | DA809283 | NPHP1-PARG | chr2:110962588 | chr10:51363311 | |
| Chimerdb3.0 | ChiTaRs | NA | W33075 | CD109-NPHP1 | chr6:74440297 | chr2:110919178 | |
| Chimerdb3.0 | FusionScan | BRCA | TCGA-C8-A12U-01A | HSD17B7-NPHP1 | In-Frame | chr1:162762652 | chr2:110927575 |
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| TissGeneNet for NPHP1 |
| Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
| BRCA (tumor) | BRCA (normal) |
| NPHP1, ERLIN2, FLNB, VCP, FLNA, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, DCUN1D1, UBQLN4, STARD13, ASAP1, INVS, INSIG1, TNK2, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, MED28, PTK2B, DCUN1D1, UBQLN4, STARD13, ASAP1, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| COAD (tumor) | COAD (normal) |
| NPHP1, ERLIN2, FLNB, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, UBQLN4, STARD13, ASAP1, FLNC, INVS, INSIG1, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, FLNA, BCAR1, KHDRBS1, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, UBQLN4, STARD13, ASAP1, INVS, INSIG1, TNK2, NPHP3 (normal) |
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| HNSC (tumor) | HNSC (normal) |
| NPHP1, ERLIN2, VCP, FLNA, BCAR1, KHDRBS1, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, DCUN1D1, UBQLN4, STARD13, ASAP1, FLNC, INVS, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, FLNA, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, PTK2B, UBQLN4, STARD13, ASAP1, INVS, INSIG1, NPHP4, NPHP3 (normal) |
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| KICH (tumor) | KICH (normal) |
| NPHP1, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TNS1, PAK2, MED28, RNF139, PTK2B, DCUN1D1, STARD13, ASAP1, FLNC, INVS, TNK2, NPHP4 (tumor) | NPHP1, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ADAM15, TUBB, PAK2, MED28, RNF139, PTK2B, DCUN1D1, UBQLN4, STARD13, ASAP1, INVS, INSIG1, NPHP4, NPHP3 (normal) |
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| KIRC (tumor) | KIRC (normal) |
| NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TNS1, PAK2, MED28, RNF139, DCUN1D1, UBQLN4, ASAP1, FLNC, INVS, TNK2, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, BCAR1, KHDRBS1, AMFR, ARHGAP32, TNS1, PAK2, MED28, PTK2B, DCUN1D1, UBQLN4, STARD13, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| KIRP (tumor) | KIRP (normal) |
| NPHP1, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TNS1, MED28, RNF139, PTK2B, DCUN1D1, STARD13, ASAP1, FLNC, INVS, INSIG1, NPHP4, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, AMFR, ARHGAP32, ADAM15, PAK2, MED28, RNF139, PTK2B, DCUN1D1, UBQLN4, ASAP1, FLNC, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| LIHC (tumor) | LIHC (normal) |
| NPHP1, ERLIN2, FLNB, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, RNF139, DCUN1D1, UBQLN4, STARD13, ASAP1, FLNC, INVS, INSIG1, NPHP3 (tumor) | NPHP1, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ADAM15, TUBB, TNS1, MED28, PTK2B, UBQLN4, STARD13, ASAP1, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| LUAD (tumor) | LUAD (normal) |
| NPHP1, ERLIN2, FLNB, VCP, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, PTK2B, STARD13, ASAP1, FLNC, INSIG1, TNK2, NPHP4, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, BCAR1, AMFR, ADAM15, TUBB, TNS1, PAK2, MED28, PTK2B, UBQLN4, STARD13, ASAP1, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| LUSC (tumor) | LUSC (normal) |
| NPHP1, ERLIN2, FLNB, VCP, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, RNF139, PTK2B, UBQLN4, STARD13, ASAP1, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, BCAR1, KHDRBS1, ARHGAP32, ADAM15, TNS1, PAK2, MED28, PTK2B, DCUN1D1, UBQLN4, STARD13, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| PRAD (tumor) | PRAD (normal) |
| NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, KHDRBS1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, RNF139, DCUN1D1, STARD13, ASAP1, FLNC, INVS, INSIG1, TNK2, NPHP3 (tumor) | NPHP1, FLNB, VCP, FLNA, BCAR1, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, DCUN1D1, UBQLN4, STARD13, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| STAD (tumor) | STAD (normal) |
| NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, KHDRBS1, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, STARD13, ASAP1, FLNC, INVS, NPHP4, NPHP3 (tumor) | NPHP1, ERLIN2, FLNB, VCP, FLNA, BCAR1, KHDRBS1, ARHGAP32, ADAM15, TUBB, TNS1, RNF139, PTK2B, STARD13, ASAP1, FLNC, INVS, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| THCA (tumor) | THCA (normal) |
| NPHP1, ERLIN2, FLNB, VCP, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, RNF139, PTK2B, DCUN1D1, UBQLN4, STARD13, FLNC, INVS, TNK2, NPHP4, NPHP3 (tumor) | NPHP1, ERLIN2, VCP, FLNA, BCAR1, AMFR, ARHGAP32, ADAM15, TUBB, TNS1, PAK2, MED28, PTK2B, UBQLN4, STARD13, ASAP1, FLNC, INSIG1, TNK2, NPHP4, NPHP3 (normal) |
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| TissGeneProg for NPHP1 |
| Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
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| Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
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| TissGeneClin for NPHP1 |
| TissGeneDrug for NPHP1 |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for NPHP1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0687120 | Nephronophthisis | 25 | BeFree |
| umls:C1855681 | Nephronophthisis, familial juvenile | 16 | BeFree,CLINVAR,CTD_human,UNIPROT |
| umls:C0431399 | Familial aplasia of the vermis | 13 | BeFree,GAD |
| umls:C0020258 | Hydrocephalus, Normal Pressure | 11 | BeFree |
| umls:C0000768 | Congenital Abnormality | 3 | BeFree |
| umls:C0022658 | Kidney Diseases | 2 | BeFree,CTD_human |
| umls:C0035078 | Kidney Failure | 2 | BeFree |
| umls:C0035304 | Retinal Degeneration | 2 | BeFree,LHGDN |
| umls:C1691228 | Cystic Kidney Diseases | 2 | BeFree |
| umls:C0017668 | Focal glomerulosclerosis | 1 | BeFree |
| umls:C0020503 | Hyperparathyroidism, Secondary | 1 | GAD |
| umls:C0022661 | Kidney Failure, Chronic | 1 | BeFree |
| umls:C0022680 | Polycystic Kidney Diseases | 1 | GAD |
| umls:C0025362 | Mental Retardation | 1 | BeFree |
| umls:C0026827 | Muscle hypotonia | 1 | BeFree |
| umls:C0027707 | Nephritis, Interstitial | 1 | GAD |
| umls:C0235031 | Neurologic Symptoms | 1 | BeFree |
| umls:C0242383 | Age related macular degeneration | 1 | BeFree,GAD |
| umls:C0403553 | Renal dysplasia and retinal aplasia (disorder) | 1 | BeFree,CLINVAR,CTD_human,ORPHANET |
| umls:C0431716 | Nephronophthisis - medullary cystic disease | 1 | BeFree |
| umls:C0543874 | Apraxia, oculomotor, Cogan type | 1 | BeFree |
| umls:C0600518 | Choroidal Neovascularization | 1 | GAD |
| umls:C0752166 | Bardet-Biedl Syndrome | 1 | BeFree,ORPHANET |
| umls:C1865872 | NEPHRONOPHTHISIS 2 | 1 | BeFree |
| umls:C3489733 | Oculomotor apraxia | 1 | BeFree |
| umls:C1846790 | JOUBERT SYNDROME 4 (disorder) | 0 | CLINVAR,CTD_human |
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