| Variant ID | 1138 |
|---|---|
| Entrez Gene ID | 147719 |
| Gene | LYPD4 (GeneCards) |
| Location | hg19 19:42343340-42343340
hg38 19:41839266-41839266 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| Method | HiSeq 2500 |
| Mutation(HGVS format) | NC_000019.9:g.42343340 C>T (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 7 |
| Amino acid changes in protein | R > K |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NA |
| mRNA length | NA |
| Reference length | 59128983 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | -0.6267 |
| CADD Raw score (version 1.3) | 1.06749 (Deleterious) |
| FATHMM raw prediction score | 0.04797 (Tolerated) |
| SIFT score | 0.623 (Tolerated) |
| LRT score | 0.759 (Tolerated) |
| MutationTaster score | 1 (Tolerated) |
| MutatioinAssessor score | 2.19 (Deleterious) |
| PROVEAN score | -0.64 (Tolerated) |
| MetaSVM score | -1.011 (Tolerated) |
| MetaLR score | 0.028 (Tolerated) |
| MCAP score | 0.004 (Tolerated) |
| FitCons score | 0.447 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 2.87 |
| PhyloP score based on multiple alignment of 100 vertebrates | 0.084 |
| PhastCons score based on multiple alignment of 100 vertebrates | 0 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 7.146 |
| Deleterious probability by iFish2 | 0.4086 (Neutral) |
| Deleterious probability by DeFine | 0.666 (Deleterious) |
| Entrez Gene ID | 147719 (NCBI Gene) |
|---|---|
| Official Gene Symbol | LYPD4 (GeneCards) |
| Number of variants in LYPD4 in this database | 1 (view all the variants) |
| Full name | LY6/PLAUR domain containing 4 |
| Band | 19q13.2 |
| Other IDs | Vega: OTTHUMG00000182674 HGNC: HGNC:28659 Ensembl: ENSG00000273111 |
| Other names | SMR |
| Summary | None |
| 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; |