| Variant ID | 21521 |
|---|---|
| Entrez Gene ID | 11122 |
| Gene | PTPRT (GeneCards) |
| Location | hg19 20:40827929-40827929
hg38 20:42199289-42199289 |
| Disease | Xeroderma Pigmentosum (view all the variants in this disease) |
| Method | HiSeq X Ten |
| Mutation(HGVS format) | NC_000020.10:g.40827929 G>T (Genome Assembly: GRCh37) |
| Exon or Intron | NA |
|---|---|
| Position in protein | NA |
| Amino acid changes in protein | NA > NA |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NA |
| mRNA length | NA |
| Reference length | 63025520 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | -0.7274 |
| CADD Raw score (version 1.3) | 1.906618 (Deleterious) |
| FATHMM raw prediction score | 0.69973 (Tolerated) |
| SIFT score | 0.054 (Tolerated) |
| LRT score | 0.034 (Tolerated) |
| MutationTaster score | 0.999 (Tolerated) |
| MutatioinAssessor score | 0 (Tolerated) |
| PROVEAN score | -1.14 (Tolerated) |
| MetaSVM score | -1.024 (Tolerated) |
| MetaLR score | 0.035 (Tolerated) |
| MCAP score | 0.007 (Tolerated) |
| FitCons score | 0.595 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | -0.73 |
| PhyloP score based on multiple alignment of 100 vertebrates | 0.594 |
| PhastCons score based on multiple alignment of 100 vertebrates | 0.998 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 9.323 |
| Deleterious probability by iFish2 | 0.0171 (Neutral) |
| Deleterious probability by DeFine | 0.9116 (Deleterious) |
| Entrez Gene ID | 11122 (NCBI Gene) |
|---|---|
| Official Gene Symbol | PTPRT (GeneCards) |
| Number of variants in PTPRT in this database | 53 (view all the variants) |
| Full name | protein tyrosine phosphatase, receptor type T |
| Band | 20q12-q13.11 |
| Other IDs | Vega: OTTHUMG00000033040 OMIM: 608712 HGNC: HGNC:9682 Ensembl: ENSG00000196090 |
| Other names | RPTPrho |
| Summary | The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracellular catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains a meprin-A5 antigen-PTP (MAM) domain, Ig-like and fibronectin type III-like repeats. The protein domain structure and the expression pattern of the mouse counterpart of this PTP suggest its roles in both signal transduction and cellular adhesion in the central nervous system. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008] |
| Individual ID | 29217584.22 (view all the variants in this individual) |
|---|---|
| Pubmed ID | 29217584 |
| Whose mosaic mutation | Female Patient |
| Phenotype | 3 |
| Disease | Xeroderma Pigmentosum (view all the variants in this disease) |
| OMIM ID | 278700 |
| Pubmed ID | 29217584 |
|---|---|
| Title | Aging and neurodegeneration are associated with increased mutations in single human neurons. |
| Journal | Science |
| Publication date | 2018.02 |
| Disease | Cockayne syndrome Xeroderma Pigmentosum |
| Number of cases | Male cases: 3; Female cases: 6; cases of unknown sex: 15; |