GeVIR Banner

Export Results to CSV Clear Search

Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
PTPRA ENST00000380393 16.15 5.39 8.17 1.49 3.05 2.61 0.80 0.33 0.37
ATAT1 ENST00000330083 16.15 44.82 28.64 1.49 0.68 0.80 0.80 1.97 1.34
TAF7 ENST00000313368 16.16 20.69 16.23 1.49 1.47 1.71 0.80 0.79 0.65
TOX ENST00000361421 16.16 5.62 8.25 1.49 2.97 2.57 0.80 0.33 0.37
MED24 ENST00000394128 16.17 35.63 23.93 1.48 0.78 1.09 0.80 1.58 1.04
FAM92A1 ENST00000518322 16.17 60.43 36.39 1.48 0.53 0.84 0.80 1.41 1.87
HIST1H3B ENST00000244661 16.18 96.39 55.96 1.48 0.22 0.49 0.80 0.19 1.76
ZCCHC14 ENST00000268616 16.18 13.43 12.39 1.47 2.05 2.21 0.80 0.60 0.50
RPS10 ENST00000326199 16.19 14.43 12.82 1.48 2.05 2.11 0.80 0.61 0.52
FBXL17 ENST00000542267 16.19 2.96 6.93 1.48 3.48 2.90 0.80 0.29 0.33
SMAP2 ENST00000372718 16.20 28.56 20.51 1.48 1.16 1.49 0.80 1.27 0.89
WDR1 ENST00000499869 16.20 3.92 7.44 1.48 3.29 2.80 0.80 0.31 0.34
PITPNM2 ENST00000320201 16.21 3.55 7.24 1.48 3.38 2.81 0.80 0.30 0.33
CDC42BPA ENST00000366769 16.21 10.28 10.89 1.48 2.28 2.21 0.80 0.49 0.44
HM13 ENST00000398174 16.22 20.63 16.24 1.48 1.46 1.71 0.80 0.78 0.65
ACOT7 ENST00000377855 16.22 20.39 16.10 1.48 1.43 1.70 0.80 0.76 0.66
PKIA ENST00000396418 16.23 88.25 51.36 1.48 0.23 0.63 0.80 0.37 1.90
WNT8B ENST00000343737 16.23 34.13 23.28 1.49 0.84 1.19 0.80 1.54 1.00
DPYSL3 ENST00000343218 16.24 7.01 9.02 1.49 2.58 2.43 0.80 0.37 0.38
CYSTM1 ENST00000261811 16.24 48.78 30.77 1.49 0.63 0.78 0.80 2.01 1.49
PTH1R ENST00000313049 16.25 19.59 15.72 1.49 1.43 1.77 0.80 0.74 0.66
FAM3C ENST00000359943 16.25 36.32 24.33 1.48 0.82 1.09 0.80 1.62 1.07
EDNRB ENST00000377211 16.26 29.60 21.04 1.48 1.10 1.43 0.80 1.39 0.89
CDKN3 ENST00000335183 16.26 44.17 28.40 1.48 0.61 0.78 0.81 1.95 1.29
NTF3 ENST00000423158 16.27 19.72 15.79 1.48 1.43 1.77 0.81 0.74 0.66

Cookies disclaimer

I agree Our site saves small pieces of text information (cookies) on your device in order to deliver better content and for statistical purposes. You can disable the usage of cookies by changing the settings of your browser. By browsing our website without changing the browser settings you grant us permission to store that information on your device.