Chr :
chr19
Position :
35848087
Ref Allele :
C
Alt Allele :
T
AAChange refGene :
NPHS1:NM_004646:exon11:c.G1394A:p.C465Y
UCSC :
chr19-35848087-C-T
OMIM :
NPHS1
dbSNP :
rs386833881
Gene Function :
exonic
Exonic Function :
nonsynonymous SNV

Clinical annotations are based on clinvar version 2019-03-05.

Disease condition(s) :
Finnish_congenital_nephrotic_syndrome
Clinical significance :
Likely_pathogenic
SIFT : Deleterious
Polyphen2 HDIV : Probably Damaging
Polyphen2 HVAR : Probably Damaging
LRT : Deleterious
MutationTaster : Disease Causing
MutationAssessor : Medium
FATHMM : Deleterious
PROVEAN : D
VEST3 score : 0.985
VEST3 rankscore : 0.992
MetaSVM : Deleterious
MetaLR : Deleterious
M-CAP : D
REVEL score : 0.928
REVEL rankscore : 0.983
MutPred score : 0.95
MutPred rankscore : 0.994
CADD : 27.5
DANN score : 0.998
DANN rankscore : 0.866
fathmm MKL coding : D
Eigen coding or noncoding : c
Eigen raw : 0.831
Eigen PC raw : 0.775
GenoCanyon score : 1
GenoCanyon score rankscore : 0.448
integrated fitCons score : 0.646
integrated fitCons score rankscore : 0.45
integrated confidence value : 0
GERP++ RS : 5.04
GERP++_RS rankscore : 0.672
phyloP100way vertebrate : 5.414
phyloP100way vertebrate rankscore : 0.659
phyloP20way mammalian : 0.852
phyloP20way mammalian rankscore : 0.362
phastCons100way vertebrate : 1
phastCons100way vertebrate rankscore : 0.715
phastCons20way mammalian : 0.999
phastCons20way mammalian rankscore : 0.75
SiPhy 29way logOdds : 15.941
SiPhy 29way logOdds rankscore : 0.795
IndiGen Frequencies
  • Allele Count :    1
  • Allele Frequency :    0.0005
  • Allele Number :    2042
  • Homozygous :    0
  • Heterozygous :    1
1000 Genome
All AFR AMR EAS SAS EUR
- - - - - -
gnomAD
All AFR AMR EAS SAS AMI ASJ FIN NFE OTH
- - - - - - - - - -
GME
All NWA NEA AP Israel SD TP CA
- - - - - - - -
Esp6500
All
-

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