PopViz

Integrative and interactive webserver for visualizing population genetics (based on gnomAD) and mutation damage prediction scores of human gene variants
 
REFERENCE: P. Zhang, et al. PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations, Bioinformatics, 2018 (suppl)


Search Options


Human Reference Genome:    GRCh37/hg19     GRCh38/hg38

Visulization Components: 
X-Axis
MAF  (General, in gnomAD)
MAF  (Maximum, in gnomAD)
Amino Acid Position
Y-Axis
CADD  (Phred-like Score)
EIGEN  (Phred-like Score)
LINSIGHT  (Probability)
MAF  (General, in gnomAD)
MAF  (Maximum, in gnomAD)

MAF Range: -
Disease Information:
Mode of Inheritance: AD     AR    
Disease Prevalence: (in decimal)
Population: (based on gnomAD)
General   (123,136 exomes)
AFR: African / African American  (7,652 exomes)
AMR: Admixed American / Latino  (16,791 exomes)
ASJ: Ashkenazi Jewish  (4,925 exomes)
EAS: East Asian  (8,624 exomes)
FIN: Finnish  (11,150 exomes)
NFE: Non-Finnish European  (55,860 exomes)
SAS: South Asian  (15,391 exomes)

Mutation Consequence:
All
3-UTR
5-UTR
Frameshift
Inframe Deletion
Inframe Insertion
Intronic
Missense
Splice Acceptor
Splice Donor
Splice Region
Start Lost
Stop Gained
Stop Lost
Synonymous

Gene-Level Cutoff on CADD Score:
None
MSC (Mutation Significance Cutoff) at 99%  95%  90%  Confidence Internval

Mutation Impact:    All     High     Moderate     Modifier     Low

Loss of Function:     All     High-Confidence     Low-Confidence

Only the Variants in More Than 1 Individual (AC > 1)

Only the Variants Having Homozygous Alleles (HOM > 1)

Only the Variants Having Hemizygous Alleles, for Sex-Linked Genes (HEMI > 1)


User's Mutations? :    No    Yes

Please provide the first 5 columns of the mutations (<= 100) in VCF format. If ID is empty, fill it by a dot.




About Us

  Developer  |  Peng ZHANG (Ph.D.)

  Artwork  |  Zhou YANG (B.A.)

  Development Team  |  Yuval ITAN (Ph.D.), Bertrand BOISSON (Ph.D.), Laurent ABEL (Ph.D.)

  Lab Head  |  Jean-Laurent CASANOVA (M.D., Ph.D.)

  Lab  |  St. Giles Laboratory of Human Genetics of Infectious Diseases

  Address  |  The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA

  Last Update  |  July 04, 2018

  Publication  |  P. Zhang, B. Bigio, F. Rapaport, S.Y. Zhang, J.L. Casanova, L. Abel, B. Boisson, and Y. Itan. PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations, Bioinformatics, 2018 (Supplementary Document)

  Web Visits  |