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
MGMT ENST00000306010 87.68 89.26 91.37 0.23 0.27 0.15 0.37 0.36 0.18
LDHAL6B ENST00000307144 87.69 79.11 86.60 0.23 0.39 0.30 0.37 0.69 0.33
URB1 ENST00000382751 87.69 30.00 58.96 0.23 1.09 0.49 0.37 1.42 1.65
GPR31 ENST00000366834 87.70 94.04 93.64 0.23 0.25 0.13 0.37 0.26 0.15
KRTAP13-4 ENST00000334068 87.70 92.85 93.02 0.23 0.29 0.14 0.37 0.30 0.15
IL27RA ENST00000263379 87.71 46.83 69.44 0.23 0.71 0.43 0.37 1.97 0.98
EFNA2 ENST00000215368 87.71 66.85 80.61 0.23 0.53 0.39 0.37 1.24 0.52
FCAMR ENST00000324852 87.72 65.04 79.67 0.23 0.52 0.38 0.37 1.24 0.53
LIPM ENST00000404743 87.72 67.96 81.17 0.23 0.52 0.38 0.37 1.17 0.49
KLHL34 ENST00000379499 87.73 76.64 85.54 0.23 0.42 0.33 0.37 0.83 0.35
ATP6V0E2 ENST00000421974 87.73 65.01 79.69 0.23 0.49 0.38 0.37 1.24 0.53
OR1L1 ENST00000309623 87.74 90.78 92.00 0.23 0.25 0.14 0.37 0.35 0.16
ZNF285 ENST00000330997 87.74 70.26 82.38 0.23 0.52 0.33 0.37 1.12 0.44
AC006435.1 ENST00000609667 87.75 96.61 94.93 0.23 0.23 0.09 0.37 0.20 0.11
MICALL2 ENST00000297508 87.75 75.52 84.99 0.23 0.44 0.33 0.37 0.90 0.39
SH2D7 ENST00000328828 87.76 59.99 77.02 0.23 0.53 0.37 0.37 1.37 0.61
ARHGEF33 ENST00000409978 87.76 31.50 60.06 0.23 0.96 0.47 0.37 1.43 1.61
IL17C ENST00000244241 87.77 86.77 90.31 0.23 0.24 0.15 0.37 0.40 0.21
TTC24 ENST00000368236 87.77 51.02 72.01 0.23 0.65 0.42 0.37 1.92 0.81
BPI ENST00000262865 87.78 68.63 81.55 0.23 0.53 0.35 0.37 1.18 0.48
C8G ENST00000224181 87.78 94.44 93.89 0.23 0.23 0.09 0.37 0.24 0.11
FUT3 ENST00000303225 87.79 97.01 95.13 0.23 0.24 0.09 0.37 0.19 0.10
ARHGAP40 ENST00000373345 87.80 42.66 66.97 0.23 0.59 0.53 0.37 1.90 1.19
S100A7 ENST00000368723 87.80 82.34 88.24 0.23 0.34 0.23 0.37 0.52 0.30
SLFN11 ENST00000394566 87.81 81.96 88.04 0.23 0.35 0.24 0.37 0.50 0.31

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.