Overview

Variant ID 927
Entrez Gene ID 374308
Gene PTCHD3 (GeneCards)
Location hg19 10:27702651-27702651
hg38 10:27413722-27413722
Disease Human Skin Fibroblasts (view all the variants in this disease)
Method HiSeq 2500
Mutation(HGVS format) NC_000010.10:g.27702651 G>A (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Position in protein 177
Amino acid changes in protein P > S
Position in cDNA NA
Changes in cDNA NA > NA
mRNA accession NA
mRNA length NA
Reference length 135534747

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
EIGEN score 0.2763
CADD Raw score (version 1.3) 3.357462 (Deleterious)
FATHMM raw prediction score 0.66925 (Tolerated)
SIFT score 0.08 (Tolerated)
LRT score 0.04 (Tolerated)
MutationTaster score 0.974 (Deleterious)
MutatioinAssessor score 2.695 (Deleterious)
PROVEAN score -5.09 (Deleterious)
MetaSVM score 0.481 (Deleterious)
MetaLR score 0.713 (Deleterious)
MCAP score 0.081 (Deleterious)
FitCons score 0.556 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 3.77
PhyloP score based on multiple alignment of 100 vertebrates 3.369
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 13.95
Deleterious probability by iFish2 0.7443 (Deleterious)
Deleterious probability by DeFine 0.9536 (Deleterious)
Entrez Gene ID 374308 (NCBI Gene)
Official Gene Symbol PTCHD3 (GeneCards)
Number of variants in PTCHD3 in this database 3 (view all the variants)
Full name patched domain containing 3
Band 10p12.1
Other IDs Vega: OTTHUMG00000017860
OMIM: 611791
HGNC: HGNC:24776
Ensembl: ENSG00000182077
Other names PTR
Summary None

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;