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
CLEC4C ENST00000542353 97.26 72.15 87.81 0.10 0.52 0.24 0.11 1.04 0.32
DEFB126 ENST00000382398 98.55 85.09 94.55 0.10 0.25 0.09 0.11 0.45 0.12
ZNF836 ENST00000322146 97.26 96.86 99.02 0.10 0.23 0.11 0.11 0.19 0.04
PAGE2 ENST00000374968 98.55 83.85 93.99 0.10 0.28 0.09 0.11 0.47 0.11
GLIPR1L1 ENST00000312442 97.27 76.98 90.18 0.10 0.43 0.18 0.11 0.79 0.21
SPATA31D1 ENST00000344803 98.56 77.90 91.19 0.10 0.42 0.15 0.11 0.79 0.18
KLK4 ENST00000324041 97.27 73.92 88.72 0.10 0.53 0.20 0.11 1.02 0.28
C6orf195 ENST00000296847 98.56 99.71 99.92 0.10 0.17 0.12 0.11 0.11 0.04
HRASLS2 ENST00000255695 97.28 90.74 96.81 0.10 0.25 0.08 0.11 0.35 0.07
LCN10 ENST00000497771 98.57 73.56 89.16 0.10 0.52 0.19 0.11 1.03 0.25
LRRC27 ENST00000368614 97.28 74.41 88.97 0.10 0.53 0.19 0.11 1.00 0.28
OR2T3 ENST00000359594 97.29 99.76 99.38 0.10 0.17 0.11 0.11 0.11 0.04
DDTL ENST00000215770 98.57 91.57 97.66 0.10 0.23 0.09 0.11 0.33 0.06
CMTM1 ENST00000379500 97.29 71.23 87.41 0.10 0.53 0.28 0.11 1.06 0.31
ZNF418 ENST00000396147 98.58 80.20 92.08 0.10 0.37 0.14 0.11 0.59 0.16
ZNF765 ENST00000396408 97.30 96.74 98.98 0.10 0.23 0.11 0.11 0.19 0.04
IL32 ENST00000525643 98.58 95.80 99.08 0.10 0.22 0.11 0.11 0.20 0.04
OR2M3 ENST00000456743 97.30 97.77 99.27 0.10 0.21 0.11 0.11 0.17 0.04
ZNF114 ENST00000595607 98.59 92.25 97.90 0.10 0.25 0.09 0.11 0.31 0.04
GCNT6 ENST00000417671 97.31 56.61 80.29 0.10 0.53 0.38 0.11 1.55 0.52
MAGEA10 ENST00000370323 98.60 99.94 99.75 0.10 0.18 0.12 0.11 0.10 0.04
KLRC3 ENST00000381903 97.31 86.43 94.58 0.10 0.24 0.09 0.11 0.42 0.11
PRNT ENST00000326539 97.32 97.61 99.72 0.10 0.22 0.12 0.11 0.20 0.04
BLACE ENST00000378120 98.60 97.53 99.53 0.10 0.22 0.12 0.11 0.19 0.05
PTPRCAP ENST00000326294 97.32 69.42 86.57 0.10 0.56 0.30 0.11 1.13 0.33

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.