| Variant ID | 786 |
|---|---|
| Entrez Gene ID | 2731 |
| Gene | GLDC (GeneCards) |
| Location | hg19 9:6589240-6589240
hg38 9:6589240-6589240 |
| Disease | Human Skin Fibroblasts (view all the variants in this disease) |
| Method | HiSeq 2500 |
| Mutation(HGVS format) | NC_000009.11:g.6589240 A>C (Genome Assembly: hg19) |
| Exon or Intron | Exon |
|---|---|
| Position in protein | 512 |
| Amino acid changes in protein | V > G |
| 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 | -1.0071 |
| CADD Raw score (version 1.3) | -0.267416 (Deleterious) |
| FATHMM raw prediction score | 0.90745 (Tolerated) |
| SIFT score | 0.491 (Tolerated) |
| LRT score | 0.068 (Tolerated) |
| MutationTaster score | 0.995 (Deleterious) |
| MutatioinAssessor score | -0.62 (Tolerated) |
| PROVEAN score | 0.05 (Tolerated) |
| MetaSVM score | 0.309 (Deleterious) |
| MetaLR score | 0.789 (Deleterious) |
| MCAP score | 0.07 (Deleterious) |
| FitCons score | 0.516 (Highly Significant p < 0.003 ) |
| Genomic Evolutionary Rate Profiling (GERP) score | 3.61 |
| PhyloP score based on multiple alignment of 100 vertebrates | 3.563 |
| PhastCons score based on multiple alignment of 100 vertebrates | 0.979 |
| SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 11.461 |
| Deleterious probability by iFish2 | 0.0694 (Neutral) |
| Deleterious probability by DeFine | 0.9299 (Deleterious) |
| Entrez Gene ID | 2731 (NCBI Gene) |
|---|---|
| Official Gene Symbol | GLDC (GeneCards) |
| Number of variants in GLDC in this database | 3 (view all the variants) |
| Full name | glycine decarboxylase |
| Band | 9p24.1 |
| Other IDs | Vega: OTTHUMG00000019524 OMIM: 238300 HGNC: HGNC:4313 Ensembl: ENSG00000178445 |
| Other names | GCE, GCSP, HYGN1 |
| Summary | Degradation of glycine is brought about by the glycine cleavage system, which is composed of four mitochondrial protein components: P protein (a pyridoxal phosphate-dependent glycine decarboxylase), H protein (a lipoic acid-containing protein), T protein (a tetrahydrofolate-requiring enzyme), and L protein (a lipoamide dehydrogenase). The protein encoded by this gene is the P protein, which binds to glycine and enables the methylamine group from glycine to be transferred to the T protein. Defects in this gene are a cause of nonketotic hyperglycinemia (NKH).[provided by RefSeq, Jan 2010] |
| 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; |