| Variant ID | 918 |
|---|---|
| Entrez Gene ID | 27031 |
| Gene | NPHP3 (GeneCards) |
| Location | hg19 3:132405141-132405141
hg38 3:132686297-132686297 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| Method | HiSeq 2500 |
| Mutation(HGVS format) | NC_000003.11:g.132405141 C>T (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 1098 |
| Amino acid changes in protein | E > K |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NA |
| mRNA length | NA |
| Reference length | 198022430 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | 0.6703 |
| CADD Raw score (version 1.3) | 7.383845 (Deleterious) |
| FATHMM raw prediction score | 0.98972 (Tolerated) |
| SIFT score | 0.068 (Tolerated) |
| LRT score | 0 (Deleterious) |
| MutationTaster score | 1 (Deleterious) |
| MutatioinAssessor score | 0.735 (Tolerated) |
| PROVEAN score | -1.03 (Tolerated) |
| MetaSVM score | 0.804 (Deleterious) |
| MetaLR score | 0.806 (Deleterious) |
| MCAP score | 0.237 (Deleterious) |
| FitCons score | 0.651 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 5.69 |
| PhyloP score based on multiple alignment of 100 vertebrates | 7.508 |
| PhastCons score based on multiple alignment of 100 vertebrates | 1 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 19.819 |
| Deleterious probability by iFish2 | 0.8137 (Deleterious) |
| Deleterious probability by DeFine | 0.911 (Deleterious) |
| Entrez Gene ID | 27031 (NCBI Gene) |
|---|---|
| Official Gene Symbol | NPHP3 (GeneCards) |
| Number of variants in NPHP3 in this database | 1 (view all the variants) |
| Full name | nephrocystin 3 |
| Band | 3q22.1 |
| Other IDs | Vega: OTTHUMG00000159713 OMIM: 608002 HGNC: HGNC:7907 Ensembl: ENSG00000113971 |
| Other names | MKS7, NPH3, RHPD, RHPD1, SLSN3, CFAP31 |
| Summary | This gene encodes a protein containing a coiled-coil (CC) domain, a tubulin-tyrosine ligase (TTL) domain, and a tetratrico peptide repeat (TPR) domain. The encoded protein interacts with nephrocystin, it is required for normal ciliary development, and it functions in renal tubular development. Mutations in this gene are associated with nephronophthisis type 3, and also with renal-hepatic-pancreatic dysplasia, and Meckel syndrome type 7. Naturally occurring read-through transcripts exist between this gene and the downstream ACAD11 (acyl-CoA dehydrogenase family, member 11) gene. [provided by RefSeq, Feb 2011] |
| Individual ID | 27788131.02 (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; |