Overview

Variant ID 29580
Entrez Gene ID 10016
Gene PDCD6 (GeneCards)
Location hg19 5:306768-306768
hg38 5:306653-306653
Disease Autism Spectrum Disorders (view all the variants in this disease)
Method MiSeq
Mutation(HGVS format) NC_000005.9:g.306768 G>A (Genome Assembly: hg19)

Other information

Exon or Intron NA
Position in protein NA
Amino acid changes in protein NA > NA
Position in cDNA NA
Changes in cDNA NA > NA
mRNA accession NA
mRNA length NA
Reference length 180915260

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
SNP ID (dbSNP ID version 137) rs145515975
EIGEN score 0.2448
CADD Raw score (version 1.3) 5.12653 (Deleterious)
FATHMM raw prediction score 0.98689 (Tolerated)
SIFT score 0.006 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 0.585 (Tolerated)
PROVEAN score -2.5 (Deleterious)
MetaSVM score -0.886 (Tolerated)
MetaLR score 0.193 (Tolerated)
MCAP score 0.027 (Deleterious)
FitCons score 0.707 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 5.53
PhyloP score based on multiple alignment of 100 vertebrates 8.96
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 16.958
Deleterious probability by iFish2 0.6784 (Deleterious)
Deleterious probability by DeFine 0.9621 (Deleterious)
Entrez Gene ID 10016 (NCBI Gene)
Official Gene Symbol PDCD6 (GeneCards)
Number of variants in PDCD6 in this database 1 (view all the variants)
Full name programmed cell death 6
Band 5p15.33
Other IDs Vega: OTTHUMG00000090283
OMIM: 601057
HGNC: HGNC:8765
Ensembl: ENSG00000249915
Other names ALG2, ALG-2, PEF1B
Summary This gene encodes a calcium-binding protein belonging to the penta-EF-hand protein family. Calcium binding is important for homodimerization and for conformational changes required for binding to other protein partners. This gene product participates in T cell receptor-, Fas-, and glucocorticoid-induced programmed cell death. In mice deficient for this gene product, however, apoptosis was not blocked suggesting this gene product is functionally redundant. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene, and a pseudogene of this gene is also located on the short arm of chromosome 5. [provided by RefSeq, May 2012]

Individual #1

Individual ID 28714951.256 (view all the variants in this individual)
Pubmed ID 28714951
Whose mosaic mutation Patient  
Phenotype 3  
Disease Autism Spectrum Disorders (view all the variants in this disease)
OMIM ID 209850

Publication #1: 28714951

Pubmed ID 28714951
Title Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder
Journal Nat Neurosci
Publication date 2017.07
Disease Autism Spectrum Disorders
Incidence 0.01
Number of cases cases of unknown sex: 376;