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
CCDC121 ENST00000394775 95.30 37.10 68.18 0.10 0.78 0.49 0.11 1.67 1.08
ZNF682 ENST00000397165 95.30 80.18 90.81 0.10 0.37 0.15 0.11 0.59 0.20
CARD16 ENST00000375706 95.31 52.16 76.87 0.10 0.61 0.35 0.11 1.85 0.60
CARD8 ENST00000391898 95.32 47.70 74.39 0.10 0.61 0.40 0.11 1.98 0.71
ZNF688 ENST00000223459 95.32 85.02 92.92 0.10 0.25 0.14 0.11 0.45 0.15
FATE1 ENST00000370350 95.33 72.87 87.25 0.10 0.49 0.28 0.11 1.05 0.31
KRTAP9-1 ENST00000398470 95.33 98.05 98.80 0.10 0.20 0.10 0.11 0.16 0.05
PSPN ENST00000245810 95.34 89.13 94.98 0.10 0.27 0.09 0.11 0.35 0.10
ZSCAN5C ENST00000534327 95.34 84.30 92.56 0.10 0.28 0.14 0.11 0.44 0.15
AC007401.2 ENST00000406220 95.35 96.11 98.13 0.10 0.21 0.09 0.11 0.20 0.05
FCGR3B ENST00000531221 95.35 84.83 92.83 0.10 0.27 0.14 0.11 0.42 0.15
C16orf78 ENST00000299191 95.36 65.30 83.73 0.10 0.51 0.34 0.11 1.25 0.41
TAS2R13 ENST00000390677 95.36 98.55 99.02 0.11 0.20 0.11 0.11 0.15 0.04
GSTT2 ENST00000215780 95.37 85.84 93.31 0.11 0.28 0.13 0.11 0.43 0.15
LILRA2 ENST00000251377 95.37 88.94 94.92 0.11 0.25 0.09 0.11 0.35 0.11
IGFL3 ENST00000341415 95.38 70.96 86.36 0.11 0.49 0.33 0.11 1.05 0.33
CARD17 ENST00000375707 95.38 92.25 96.61 0.11 0.25 0.08 0.11 0.31 0.08
CD52 ENST00000374213 95.39 85.85 93.32 0.11 0.28 0.13 0.11 0.43 0.15
TNFRSF4 ENST00000379236 95.39 67.79 84.95 0.11 0.52 0.33 0.11 1.18 0.40
PRM2 ENST00000241808 95.40 78.47 90.01 0.11 0.43 0.18 0.11 0.74 0.22
ZNF492 ENST00000456783 95.40 81.93 91.54 0.11 0.35 0.15 0.11 0.51 0.18
POTEE ENST00000356920 95.41 52.99 77.40 0.11 0.66 0.35 0.11 1.78 0.58
KIAA1257 ENST00000265068 95.41 70.83 86.34 0.11 0.49 0.33 0.11 1.07 0.33
ZNF416 ENST00000196489 95.42 56.71 79.36 0.11 0.53 0.39 0.11 1.56 0.54
C8orf44 ENST00000519561 95.42 79.43 90.49 0.11 0.38 0.14 0.11 0.66 0.21

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.