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
PSMD3 ENST00000264639 18.47 1.48 7.34 1.54 3.91 2.81 0.91 0.26 0.34
C3orf58 ENST00000315691 18.48 45.96 30.43 1.54 0.76 0.80 0.91 2.03 1.46
NKX2-3 ENST00000344586 18.48 14.35 14.14 1.54 2.04 1.99 0.91 0.61 0.60
THOC3 ENST00000265097 18.49 52.44 33.62 1.54 0.65 0.90 0.91 1.83 1.72
CPD ENST00000225719 18.49 20.42 17.33 1.54 1.43 1.63 0.91 0.76 0.75
FAR2 ENST00000536681 18.50 21.72 18.03 1.54 1.46 1.70 0.91 0.81 0.78
DENND5B ENST00000389082 18.50 3.24 8.23 1.54 3.46 2.58 0.91 0.28 0.37
DOPEY1 ENST00000349129 18.51 7.87 10.78 1.54 2.54 2.19 0.91 0.44 0.43
CCDC125 ENST00000396496 18.51 57.22 35.98 1.54 0.56 0.86 0.91 1.49 1.78
EPHB1 ENST00000398015 18.52 7.84 10.76 1.54 2.56 2.19 0.91 0.44 0.43
PPP1R7 ENST00000234038 18.52 8.02 10.89 1.54 2.53 2.21 0.91 0.44 0.44
ANK1 ENST00000265709 18.53 3.32 8.27 1.54 3.42 2.57 0.91 0.27 0.37
ABHD16A ENST00000395952 18.53 18.81 16.49 1.54 1.53 1.71 0.91 0.74 0.69
MSANTD4 ENST00000301919 18.54 40.45 27.63 1.54 0.62 0.96 0.91 1.77 1.27
KIAA1045 ENST00000242315 18.54 29.71 22.29 1.56 1.11 1.16 0.91 1.39 0.96
MAST4 ENST00000403625 18.55 18.20 16.18 1.56 1.49 1.71 0.91 0.75 0.66
HOXC8 ENST00000040584 18.55 31.99 23.39 1.54 0.92 1.19 0.91 1.48 0.99
SLC1A3 ENST00000265113 18.56 11.81 12.72 1.54 2.09 2.16 0.91 0.57 0.52
GINM1 ENST00000367419 18.56 68.38 41.71 1.53 0.52 0.72 0.91 1.20 2.01
ATP5H ENST00000301587 18.57 74.09 44.98 1.53 0.53 0.68 0.91 1.03 2.04
TNFSF15 ENST00000374045 18.57 51.47 33.18 1.53 0.63 0.87 0.91 1.88 1.69
ZFY ENST00000155093 18.58 28.49 21.68 1.53 1.16 1.25 0.91 1.25 0.91
MTSS1 ENST00000518547 18.58 4.44 8.88 1.53 3.27 2.49 0.91 0.32 0.38
GRK5 ENST00000392870 18.59 17.18 15.71 1.53 1.61 1.77 0.91 0.75 0.66
PIK3R5 ENST00000447110 18.59 16.15 15.15 1.53 1.82 1.85 0.91 0.69 0.64

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.