GeVIR Banner
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
DEFB129 ENST00000246105 96.80 92.77 97.38 0.09 0.29 0.08 0.11 0.30 0.07
OR7E24 ENST00000456448 96.81 99.52 99.11 0.09 0.16 0.11 0.11 0.13 0.04
AC140481.2 ENST00000409982 96.81 85.40 93.86 0.09 0.25 0.09 0.11 0.44 0.12
XAGE5 ENST00000351072 96.82 91.83 97.07 0.09 0.23 0.08 0.11 0.32 0.07
IZUMO1 ENST00000332955 96.82 66.54 85.05 0.09 0.57 0.33 0.11 1.22 0.38
ADAM20 ENST00000256389 96.83 99.85 99.63 0.09 0.17 0.12 0.11 0.11 0.04
C19orf59 ENST00000333598 96.83 57.47 80.47 0.09 0.56 0.39 0.11 1.48 0.50
C1orf127 ENST00000377004 96.84 55.43 79.40 0.09 0.58 0.39 0.11 1.60 0.52
AC079612.1 ENST00000358775 96.84 82.42 92.32 0.09 0.34 0.14 0.11 0.52 0.15
FAM47C ENST00000358047 96.85 99.93 99.16 0.09 0.17 0.11 0.11 0.10 0.04
C21orf54 ENST00000451980 96.85 90.33 96.31 0.09 0.25 0.07 0.11 0.38 0.09
ZNF846 ENST00000397902 96.86 95.66 98.47 0.09 0.23 0.10 0.11 0.20 0.05
DYDC2 ENST00000372198 96.86 84.81 93.60 0.09 0.27 0.13 0.11 0.42 0.15
ZNF468 ENST00000595646 96.87 96.07 98.63 0.09 0.21 0.10 0.11 0.20 0.05
PRB4 ENST00000279575 98.23 97.43 99.39 0.09 0.22 0.11 0.11 0.19 0.04
ICAM3 ENST00000160262 96.88 96.42 98.71 0.09 0.22 0.10 0.11 0.19 0.05
TCEB3CL2 ENST00000591973 98.23 98.83 99.73 0.09 0.16 0.12 0.11 0.14 0.04
AC026703.1 ENST00000326958 96.88 98.95 99.13 0.09 0.17 0.11 0.11 0.15 0.04
CFHR5 ENST00000256785 96.89 91.04 96.74 0.09 0.25 0.08 0.11 0.36 0.08
MNDA ENST00000368141 98.24 91.02 97.30 0.09 0.25 0.08 0.11 0.35 0.07
C2orf83 ENST00000264387 96.89 97.14 98.98 0.09 0.24 0.11 0.11 0.18 0.04
HRNR ENST00000368801 98.24 96.50 99.17 0.09 0.22 0.11 0.11 0.19 0.04
CXXC11 ENST00000343216 96.90 95.44 98.44 0.09 0.24 0.10 0.11 0.20 0.05
SPACA7 ENST00000283550 98.25 71.28 87.88 0.09 0.53 0.24 0.11 1.07 0.32
C9orf139 ENST00000314330 96.90 94.79 98.18 0.09 0.23 0.09 0.11 0.24 0.05

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.