Chr :
chr15
Position :
42394296
Ref Allele :
G
Alt Allele :
A
AAChange refGene :
CAPN3:NM_173087:exon7:c.G926A:p.R309Q,CAPN3:NM_000070:exon8:c.G1070A:p.R357Q,CAPN3:NM_024344:exon8:c.G1070A:p.R357Q
UCSC :
chr15-42394296-G-A
OMIM :
CAPN3
dbSNP :
rs988027905
Gene Function :
exonic
Exonic Function :
nonsynonymous SNV

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

Disease condition(s) :
Limb-girdle_muscular_dystrophy,_type_2A|not_provided
Clinical significance :
Conflicting_interpretations_of_pathogenicity
SIFT : Deleterious
Polyphen2 HDIV : Probably Damaging
Polyphen2 HVAR : Probably Damaging
LRT : Unknown
MutationTaster : Disease Causing
MutationAssessor : Low
FATHMM : Deleterious
PROVEAN : D
VEST3 score : 0.978
VEST3 rankscore : 0.985
MetaSVM : Deleterious
MetaLR : Deleterious
M-CAP : D
REVEL score : 0.877
REVEL rankscore : 0.964
MutPred score : 0.93
MutPred rankscore : 0.989
CADD : 35
DANN score : 1
DANN rankscore : 1
fathmm MKL coding : D
Eigen coding or noncoding : c
Eigen raw : 0.851
Eigen PC raw : 0.855
GenoCanyon score : 1
GenoCanyon score rankscore : 0.983
integrated fitCons score : 0.638
integrated fitCons score rankscore : 0.428
integrated confidence value : 0
GERP++ RS : 5.34
GERP++_RS rankscore : 0.759
phyloP100way vertebrate : 9.626
phyloP100way vertebrate rankscore : 0.978
phyloP20way mammalian : 1.048
phyloP20way mammalian rankscore : 0.713
phastCons100way vertebrate : 1
phastCons100way vertebrate rankscore : 0.715
phastCons20way mammalian : 1
phastCons20way mammalian rankscore : 0.888
SiPhy 29way logOdds : 19.241
SiPhy 29way logOdds rankscore : 0.938
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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