Variant ID | 981 |
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Entrez Gene ID | 200576 |
Gene | PIKFYVE (GeneCards) |
Location | hg19 2:209142402-209142402
hg38 2:208277678-208277678 |
Disease | Human Skin Fibroblasts (view all the variants in this disease) |
Method | HiSeq 2500 |
Mutation(HGVS format) | NC_000002.11:g.209142402 G>A (Genome Assembly: hg19) |
Exon or Intron | Exon |
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Position in protein | 195 |
Amino acid changes in protein | E > K |
Position in cDNA | NA |
Changes in cDNA | NA > NA |
mRNA accession | NA |
mRNA length | NA |
Reference length | 243199373 |
MAF in gnomAD genome (version 2.0.1) | 0 |
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EIGEN score | 0.6332 |
CADD Raw score (version 1.3) | 6.206908 (Deleterious) |
FATHMM raw prediction score | 0.99399 (Tolerated) |
SIFT score | 0.025 (Deleterious) |
LRT score | 0 (Deleterious) |
MutationTaster score | 1 (Deleterious) |
MutatioinAssessor score | 0.3 (Tolerated) |
PROVEAN score | -1.88 (Tolerated) |
MetaSVM score | -0.959 (Tolerated) |
MetaLR score | 0.158 (Tolerated) |
MCAP score | 0.01 (Tolerated) |
FitCons score | 0.672 (Highly Significant p < 0.003 ) |
Genomic Evolutionary Rate Profiling (GERP) score | 5.78 |
PhyloP score based on multiple alignment of 100 vertebrates | 9.932 |
PhastCons score based on multiple alignment of 100 vertebrates | 1 |
SiPhy log transformed odds ratio on multiple alignment of 29 mammals | 20.008 |
Deleterious probability by iFish2 | 0.997 (Deleterious) |
Deleterious probability by DeFine | 0.9571 (Deleterious) |
Entrez Gene ID | 200576 (NCBI Gene) |
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Official Gene Symbol | PIKFYVE (GeneCards) |
Number of variants in PIKFYVE in this database | 1 (view all the variants) |
Full name | phosphoinositide kinase, FYVE-type zinc finger containing |
Band | 2q34 |
Other IDs | Vega: OTTHUMG00000132945 OMIM: 609414 HGNC: HGNC:23785 Ensembl: ENSG00000115020 |
Other names | CFD, FAB1, HEL37, PIP5K, PIP5K3, ZFYVE29 |
Summary | Phosphorylated derivatives of phosphatidylinositol (PtdIns) regulate cytoskeletal functions, membrane trafficking, and receptor signaling by recruiting protein complexes to cell- and endosomal-membranes. Humans have multiple PtdIns proteins that differ by the degree and position of phosphorylation of the inositol ring. This gene encodes an enzyme (PIKfyve; also known as phosphatidylinositol-3-phosphate 5-kinase type III or PIPKIII) that phosphorylates the D-5 position in PtdIns and phosphatidylinositol-3-phosphate (PtdIns3P) to make PtdIns5P and PtdIns(3,5)biphosphate. The D-5 position also can be phosphorylated by type I PtdIns4P-5-kinases (PIP5Ks) that are encoded by distinct genes and preferentially phosphorylate D-4 phosphorylated PtdIns. In contrast, PIKfyve preferentially phosphorylates D-3 phosphorylated PtdIns. In addition to being a lipid kinase, PIKfyve also has protein kinase activity. PIKfyve regulates endomembrane homeostasis and plays a role in the biogenesis of endosome carrier vesicles from early endosomes. Mutations in this gene cause corneal fleck dystrophy (CFD); an autosomal dominant disorder characterized by numerous small white flecks present in all layers of the corneal stroma. Histologically, these flecks appear to be keratocytes distended with lipid and mucopolysaccharide filled intracytoplasmic vacuoles. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, May 2010] |
Individual ID | 27788131.02 (view all the variants in this individual) |
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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 |
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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; |