Overview

Variant ID 981
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)

Other information

Exon or Intron Exon
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

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
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)
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 #1

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

Publication #1: 27788131

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;