Statistics

Database Statistics
Total Variant Events:309239
Total Subjects:31374
De Novo Variant Events: 271055
Loss of Function Variant Events:28859
Publications included in database:123
Last Updated:Apr 10, 2024
Genes with the most de novo loss of function variants reported
  1. SCN2A - sodium voltage-gated channel alpha subunit 2
  2. CHD8 - chromodomain helicase DNA binding protein 8
  3. ADNP - activity dependent neuroprotector homeobox
  4. SHANK3 - SH3 and multiple ankyrin repeat domains 3
  5. SYNGAP1 - synaptic Ras GTPase activating protein 1
  6. DYRK1A - dual specificity tyrosine phosphorylation regulated kinase 1A
  7. CHD2 - chromodomain helicase DNA binding protein 2
  8. POGZ - pogo transposable element derived with ZNF domain
  9. MECP2 - methyl-CpG binding protein 2
  10. ASXL3 - additional sex combs like 3, transcriptional regulator
Genes by number of reports from distinct papers
  1. SCN2A - sodium voltage-gated channel alpha subunit 2
  2. CHD8 - chromodomain helicase DNA binding protein 8
  3. SYNGAP1 - synaptic Ras GTPase activating protein 1
  4. DYRK1A - dual specificity tyrosine phosphorylation regulated kinase 1A
  5. ARID1B - AT-rich interaction domain 1B
  6. ADNP - activity dependent neuroprotector homeobox
  7. MECP2 - methyl-CpG binding protein 2
  8. PTEN - phosphatase and tensin homolog
  9. ANK2 - ankyrin 2
  10. POGZ - pogo transposable element derived with ZNF domain
Genes with the most variant events reported
  1. IGSF3 - immunoglobulin superfamily member 3
  2. GXYLT1 - glucoside xylosyltransferase 1
  3. CTBP2 - C-terminal binding protein 2
  4. PABPC3 - poly(A) binding protein cytoplasmic 3
  5. HYDIN - HYDIN, axonemal central pair apparatus protein
  6. HLA-DRB1 - major histocompatibility complex, class II, DR beta 1
  7. CHD8 - chromodomain helicase DNA binding protein 8
  8. SCN2A - sodium voltage-gated channel alpha subunit 2
  9. ANK2 - ankyrin 2
  10. KMT2C - lysine methyltransferase 2C
These rankings are not intended to be used for ASD candidate gene pioritization because they do not exclude common variants and variants from targeted studies (non-coding variants are excluded from gene ranking calculations).

Variant Event Statistics

VariCarta’s variant event is a unique combination of a reference allele, its genomic location and alternative allele belonging to a single individual. The pie chart below shows the breakdown of variant events by publication of origin. Hovering over a pie chart segment will pop-up a tool tip showing the corresponding publication and the exact number of variants collected from it.

The variant events are grouped by their effect on the coding sequence of a gene. Definitions of different effects are given on the Documentation page. The effects for each variant event in the database are assigned by ANNOVAR and are shown in the Effect column in the variant table. The y-axis of the bar graph is log-scaled to facilitate readability. Hovering over a bar will pop-up a tool tip showing the exact number of variant events in that particular category.

The variant events are grouped by their genomic context. The genomic context for each variant event in the database are assigned by ANNOVAR and are shown in the Context column in the variant table. The y-axis of the bar graph is log-scaled to facilitate readability. Hovering over a bar will pop-up a tool tip showing the exact number of variant events in that particular category.

Variant Event Overlap

The heatmap below represents the overlap between variant events reported by different papers. The numbers on the diagonal represent the total number of reported variant events collected from a given paper. The numbers off the diagonal represent the number of variant events that are reported in both of the intersecting papers. Numbers >1000 are rounded to the nearest thousand and shown with “K” (e.g. 3462 variant events collected from Lim2017 are shown as “3K” on the diagonal). Hovering over a grid cell will pop-up a tool tip which shows the two intersecting papers and the exact number of overlapping variants. The overlapping variants can be accessed by clicking on the number in the grid cell. Note that we removed papers that had no overlaping variants with other papers for a more compact visualization.

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Bokeh Plot

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