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
C16orf98 ENST00000561916 81.23 90.26 88.87 0.33 0.25 0.19 0.60 0.38 0.28
TRIM34 ENST00000514226 81.23 56.04 71.07 0.33 0.49 0.43 0.60 1.55 0.86
RGS11 ENST00000397770 81.24 62.63 74.82 0.33 0.51 0.39 0.60 1.31 0.65
ZNF394 ENST00000337673 81.24 52.45 68.89 0.33 0.65 0.46 0.60 1.84 1.04
MICALCL ENST00000256186 81.25 80.59 84.21 0.33 0.37 0.34 0.60 0.57 0.42
OR5M3 ENST00000312240 81.25 95.77 91.42 0.33 0.23 0.15 0.60 0.20 0.18
LY6E ENST00000520466 81.26 59.74 73.26 0.33 0.52 0.43 0.60 1.37 0.79
YDJC ENST00000292778 81.26 56.30 71.22 0.33 0.52 0.44 0.61 1.55 0.86
OR8K5 ENST00000313447 81.27 93.45 90.40 0.33 0.28 0.15 0.61 0.28 0.21
THEM4 ENST00000368814 81.27 80.58 84.22 0.33 0.37 0.34 0.61 0.57 0.42
C5orf46 ENST00000318315 81.28 79.12 83.57 0.33 0.39 0.33 0.61 0.69 0.40
MLNR ENST00000218721 81.28 67.08 77.37 0.33 0.54 0.35 0.61 1.23 0.58
OR6B3 ENST00000319423 81.29 93.60 90.51 0.33 0.28 0.14 0.61 0.28 0.21
NLRP6 ENST00000312165 81.29 33.68 57.41 0.33 0.84 0.51 0.61 1.56 1.67
C10orf128 ENST00000474718 81.30 76.28 82.17 0.33 0.43 0.35 0.60 0.86 0.45
HMGB4 ENST00000522796 81.30 94.15 90.78 0.33 0.25 0.15 0.60 0.25 0.20
FAM173B ENST00000511437 81.31 85.08 86.39 0.33 0.25 0.32 0.60 0.45 0.33
ZNF555 ENST00000334241 81.31 56.84 71.63 0.33 0.56 0.44 0.60 1.54 0.83
AC012123.1 ENST00000426194 81.32 74.38 81.19 0.33 0.53 0.38 0.60 1.00 0.49
MSRA ENST00000317173 81.32 95.10 91.16 0.33 0.23 0.15 0.60 0.21 0.18
SEPT14 ENST00000388975 81.33 50.47 67.78 0.33 0.65 0.51 0.60 1.95 1.12
MPV17L ENST00000396385 81.33 85.69 86.69 0.33 0.27 0.30 0.60 0.44 0.33
AQP7 ENST00000297988 81.34 96.17 91.60 0.33 0.21 0.14 0.60 0.20 0.18
FAM213B ENST00000419916 81.34 79.89 83.91 0.33 0.37 0.35 0.60 0.61 0.43
IFNAR1 ENST00000270139 81.35 66.36 76.98 0.33 0.54 0.37 0.60 1.20 0.61

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.