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
CCIN ENST00000335119 27.51 34.52 29.17 1.23 0.80 0.84 1.41 1.56 1.32
NCEH1 ENST00000538775 27.51 36.62 30.25 1.21 0.77 0.84 1.41 1.64 1.44
TMEM30A ENST00000230461 27.52 40.86 32.40 1.21 0.61 0.91 1.41 1.78 1.61
MED22 ENST00000491289 27.52 62.99 43.61 1.21 0.48 0.59 1.41 1.31 2.01
LUC7L ENST00000293872 27.53 21.50 22.69 1.21 1.42 1.18 1.41 0.79 0.97
LRRC1 ENST00000370888 27.53 15.30 19.38 1.21 1.90 1.54 1.41 0.67 0.85
ZMAT3 ENST00000311417 27.54 54.56 39.40 1.21 0.59 0.78 1.41 1.66 2.04
FAM57B ENST00000380495 27.55 26.74 25.23 1.21 1.21 1.05 1.41 1.12 1.15
BATF3 ENST00000243440 27.55 72.35 48.85 1.21 0.51 0.71 1.41 1.03 1.85
PXDN ENST00000252804 27.56 25.46 24.56 1.23 1.25 1.06 1.41 1.05 1.09
NTAN1 ENST00000287706 27.56 60.67 42.37 1.23 0.54 0.68 1.41 1.41 2.02
ZPBP ENST00000046087 27.57 41.69 32.81 1.23 0.61 0.85 1.41 1.80 1.65
EEA1 ENST00000322349 27.57 12.90 18.18 1.23 2.07 1.64 1.41 0.59 0.79
EML1 ENST00000334192 27.58 11.01 17.13 1.23 2.10 1.64 1.41 0.52 0.73
PRDM11 ENST00000424263 27.58 12.94 18.21 1.23 2.06 1.64 1.41 0.59 0.79
SLC2A12 ENST00000275230 27.59 47.62 35.73 1.23 0.62 0.85 1.42 1.98 1.78
TNFAIP8 ENST00000504771 27.59 52.57 38.38 1.23 0.67 0.84 1.41 1.82 2.04
CACUL1 ENST00000369151 27.60 14.96 19.27 1.23 1.92 1.53 1.41 0.64 0.85
FAM192A ENST00000309137 27.60 31.44 27.67 1.23 0.96 0.95 1.41 1.42 1.27
NDFIP2 ENST00000218652 27.61 19.91 21.88 1.23 1.44 1.21 1.41 0.73 0.95
STOX2 ENST00000308497 27.61 8.69 15.98 1.23 2.48 1.77 1.41 0.47 0.66
LNPEP ENST00000231368 27.62 7.68 15.46 1.23 2.52 1.81 1.42 0.42 0.67
RAB39A ENST00000320578 27.62 65.67 45.34 1.23 0.53 0.70 1.42 1.22 1.99
NR1H4 ENST00000551379 27.63 31.54 27.74 1.23 0.96 0.90 1.42 1.42 1.27
ST3GAL6 ENST00000394162 27.63 66.43 45.72 1.24 0.56 0.67 1.42 1.20 1.99

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.