Overview

Variant ID 100
Entrez Gene ID 57526
Gene PCDH19 (GeneCards)
Location hg19 X:99662577-99662577
hg38 X:100407579-100407579
Disease Early infantile epileptic encephalopathy9 (view all the variants in this disease)
Method ABI3130XL
Mutation(HGVS format) NC_000023.10:g.99662577 T>C (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Position in protein 340
Amino acid changes in protein N > S
Position in cDNA 1019
Changes in cDNA A > G
mRNA accession NM_001184880.1
mRNA length 3447
Reference length 155270560

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
CADD Raw score (version 1.3) 4.26704 (Deleterious)
FATHMM raw prediction score 0.97724 (Tolerated)
SIFT score 0.002 (Deleterious)
LRT score 0 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 4 (Deleterious)
PROVEAN score -4.59 (Deleterious)
MetaSVM score 0.493 (Deleterious)
MetaLR score 0.59 (Deleterious)
MCAP score 0.727 (Deleterious)
Genomic Evolutionary Rate Profiling (GERP) score 5.65
PhyloP score based on multiple alignment of 100 vertebrates 8.017
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 15.009
Deleterious probability by iFish2 0.9929 (Deleterious)
Deleterious probability by DeFine 0.9793 (Deleterious)
Entrez Gene ID 57526 (NCBI Gene)
Official Gene Symbol PCDH19 (GeneCards)
Number of variants in PCDH19 in this database 24 (view all the variants)
Full name protocadherin 19
Band Xq22.1
Other IDs Vega: OTTHUMG00000022000
OMIM: 300460
HGNC: HGNC:14270
Ensembl: ENSG00000165194
Other names EFMR, EIEE9
Summary The protein encoded by this gene is a member of the delta-2 protocadherin subclass of the cadherin superfamily. The encoded protein is thought to be a calcium-dependent cell-adhesion protein that is primarily expressed in the brain. Mutations in this gene on human chromosome X are associated with sporadic infantile epileptic encephalopathy and to a female-restricted form of epilepsy (EFMR; also known as PCDH19RE). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]

Individual #1

Individual ID 22949144.01 (view all the variants in this individual)
Pubmed ID 22949144
Whose mosaic mutation Mother  
Phenotype 1  
Number of affected children 1 ( female: 1; )
Disease Early infantile epileptic encephalopathy9 (view all the variants in this disease)
OMIM ID 300088

Publication #1: 22949144

Pubmed ID 22949144
Title Somatic mosaicism of PCDH19 mutation in a family with low penetrance EFMR
Journal Neurogenetics
Publication date 2012.11
Disease Early infantile Epileptic encephalopathy9
Number of cases Female cases: 1;