| Variant ID | 1010 |
|---|---|
| Entrez Gene ID | 23230 |
| Gene | VPS13A (GeneCards) |
| Location | hg19 9:79929022-79929022
hg38 9:77314106-77314106 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| Method | HiSeq 2500 |
| Mutation(HGVS format) | NC_000009.11:g.79929022 C>T (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 1410 |
| Amino acid changes in protein | P > L |
| Position in cDNA | NA |
| Changes in cDNA | NA > NA |
| mRNA accession | NA |
| mRNA length | NA |
| Reference length | 141213431 |
| MAF in gnomAD genome (version 2.0.1) | 0 |
|---|---|
| EIGEN score | 0.3366 |
| CADD Raw score (version 1.3) | 6.106235 (Deleterious) |
| FATHMM raw prediction score | 0.83919 (Tolerated) |
| SIFT score | 0.016 (Deleterious) |
| LRT score | 0 (Deleterious) |
| MutationTaster score | 1 (Deleterious) |
| MutatioinAssessor score | 2.47 (Deleterious) |
| PROVEAN score | -3.64 (Deleterious) |
| MetaSVM score | -0.802 (Tolerated) |
| MetaLR score | 0.243 (Tolerated) |
| MCAP score | 0.028 (Deleterious) |
| FitCons score | 0.732 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 4.48 |
| PhyloP score based on multiple alignment of 100 vertebrates | 2.344 |
| PhastCons score based on multiple alignment of 100 vertebrates | 0.998 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 15.651 |
| Deleterious probability by iFish2 | 0.5125 (Deleterious) |
| Deleterious probability by DeFine | 0.8292 (Deleterious) |
| Entrez Gene ID | 23230 (NCBI Gene) |
|---|---|
| Official Gene Symbol | VPS13A (GeneCards) |
| Number of variants in VPS13A in this database | 3 (view all the variants) |
| Full name | vacuolar protein sorting 13 homolog A |
| Band | 9q21.2 |
| Other IDs | Vega: OTTHUMG00000020055 OMIM: 605978 HGNC: HGNC:1908 Ensembl: ENSG00000197969 |
| Other names | CHAC, CHOREIN |
| Summary | The protein encoded by this gene may control steps in the cycling of proteins through the trans-Golgi network to endosomes, lysosomes and the plasma membrane. Mutations in this gene cause the autosomal recessive disorder, chorea-acanthocytosis. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jul 2008] |
| 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; |