| Variant ID | 815 |
|---|---|
| Entrez Gene ID | 4867 |
| Gene | NPHP1 (GeneCards) |
| Location | hg19 2:110926046-110926046
hg38 2:110168469-110168469 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| Method | HiSeq 2500 |
| Mutation(HGVS format) | NC_000002.11:g.110926046 G>A (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 203 |
| Amino acid changes in protein | P > S |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NA |
| mRNA length | NA |
| Reference length | 243199373 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | 0.5607 |
| CADD Raw score (version 1.3) | 4.637457 (Deleterious) |
| FATHMM raw prediction score | 0.92211 (Tolerated) |
| SIFT score | 0 (Deleterious) |
| LRT score | 0 (Tolerated) |
| MutationTaster score | 0.887 (Deleterious) |
| MutatioinAssessor score | 3.97 (Deleterious) |
| PROVEAN score | -5.31 (Deleterious) |
| MetaSVM score | 0.882 (Deleterious) |
| MetaLR score | 0.892 (Deleterious) |
| MCAP score | 0.346 (Deleterious) |
| FitCons score | 0.615 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 3.62 |
| PhyloP score based on multiple alignment of 100 vertebrates | 7.505 |
| PhastCons score based on multiple alignment of 100 vertebrates | 1 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 9.547 |
| Deleterious probability by iFish2 | 0.3749 (Neutral) |
| Deleterious probability by DeFine | 0.957 (Deleterious) |
| Entrez Gene ID | 4867 (NCBI Gene) |
|---|---|
| Official Gene Symbol | NPHP1 (GeneCards) |
| Number of variants in NPHP1 in this database | 2 (view all the variants) |
| Full name | nephrocystin 1 |
| Band | 2q13 |
| Other IDs | Vega: OTTHUMG00000131195 OMIM: 607100 HGNC: HGNC:7905 Ensembl: ENSG00000144061 |
| Other names | NPH1, JBTS4, SLSN1 |
| 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 part of a multifunctional complex localized in actin- and microtubule-based structures. Mutations in this gene cause familial juvenile nephronophthisis type 1, a kidney disorder involving both tubules and glomeruli. Defects in this gene are also associated with Senior-Loken syndrome type 1, also referred to as juvenile nephronophthisis with Leber amaurosis, which is characterized by kidney and eye disease, and with Joubert syndrome type 4, which is characterized by cerebellar ataxia, oculomotor apraxia, psychomotor delay and neonatal breathing abnormalities, sometimes including retinal dystrophy and renal disease. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008] |
| Individual ID | 27788131.01 (view all the variants in this individual) |
|---|---|
| Pubmed ID | 27788131 |
| Whose mosaic mutation | Normal |
| Phenotype | 1 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| OMIM ID | 120353 |
| Pubmed ID | 27788131 |
|---|---|
| Title | The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. |
| Journal | PLoS Genetics |
| Publication date | 2016.10 |
| Disease | Human Skin Fibroblasts |
| Population | Caucasian |
| Number of cases | Male cases: 2; |