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
RHOU ENST00000366691 42.23 41.29 40.07 0.78 0.61 0.82 1.75 1.82 1.99
STXBP6 ENST00000323944 42.23 60.30 50.31 0.78 0.53 0.65 1.75 1.39 1.91
RS1 ENST00000379984 42.24 12.88 25.63 0.78 2.07 1.06 1.75 0.59 1.20
EXOSC1 ENST00000370902 42.24 78.01 60.68 0.78 0.42 0.44 1.75 0.77 1.61
TMEM214 ENST00000238788 42.25 45.06 41.86 0.78 0.67 0.68 1.75 1.97 2.02
C10orf35 ENST00000373279 42.26 80.32 62.06 0.78 0.37 0.48 1.75 0.58 1.44
BET1 ENST00000222547 42.26 83.15 63.99 0.78 0.29 0.52 1.75 0.49 1.38
KRT31 ENST00000251645 42.27 35.48 37.11 0.78 0.77 0.80 1.75 1.56 1.95
EPYC ENST00000261172 42.27 71.96 56.97 0.78 0.51 0.49 1.75 1.06 1.71
SH3RF3 ENST00000309415 42.28 24.44 31.57 0.77 1.32 0.87 1.75 1.00 1.56
CCNI2 ENST00000378731 42.28 80.90 62.45 0.77 0.35 0.48 1.75 0.57 1.39
PIWIL2 ENST00000356766 42.29 31.67 35.14 0.77 0.94 0.86 1.75 1.45 1.76
CDC14A ENST00000361544 42.29 40.82 39.92 0.76 0.61 0.80 1.75 1.78 2.01
ITGA1 ENST00000282588 42.30 37.51 38.23 0.76 0.78 0.85 1.75 1.66 2.04
RTKN ENST00000272430 42.30 41.06 40.04 0.76 0.59 0.82 1.75 1.80 1.98
PAAF1 ENST00000310571 42.31 66.66 53.97 0.76 0.56 0.61 1.75 1.22 1.77
MYSM1 ENST00000472487 42.31 19.16 28.88 0.76 1.49 0.82 1.75 0.76 1.31
TYK2 ENST00000525621 42.32 26.51 32.62 0.76 1.18 0.87 1.75 1.12 1.63
ZNF646 ENST00000300850 42.32 27.96 33.31 0.76 1.19 0.89 1.75 1.19 1.70
CLDN15 ENST00000401528 42.33 55.71 47.86 0.76 0.52 0.66 1.75 1.60 1.89
TMEM170A ENST00000561878 42.33 95.24 71.25 0.76 0.23 0.44 1.75 0.21 0.87
RRNAD1 ENST00000368216 42.34 68.55 55.03 0.76 0.53 0.51 1.75 1.19 1.73
GUCD1 ENST00000407471 42.34 34.92 36.82 0.76 0.76 0.82 1.75 1.54 1.94
ZNF395 ENST00000344423 42.35 22.24 30.54 0.76 1.53 0.80 1.75 0.81 1.47
REPS2 ENST00000357277 42.35 24.74 31.76 0.76 1.32 0.89 1.75 1.05 1.58

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.