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
C20orf173 ENST00000444723 88.46 77.16 86.05 0.20 0.43 0.33 0.35 0.78 0.33
TPSB2 ENST00000430512 88.46 94.95 94.44 0.20 0.23 0.10 0.35 0.21 0.12
CATSPER1 ENST00000312106 88.47 53.96 74.03 0.20 0.65 0.39 0.35 1.70 0.69
FAM228A ENST00000295150 88.47 59.63 77.23 0.20 0.52 0.35 0.35 1.41 0.59
LAD1 ENST00000391967 88.48 73.10 84.05 0.20 0.53 0.35 0.34 1.02 0.42
CASP10 ENST00000286186 88.48 70.44 82.85 0.20 0.52 0.32 0.34 1.08 0.42
MRAP ENST00000399784 88.49 88.34 91.32 0.20 0.23 0.15 0.34 0.37 0.18
SLC7A13 ENST00000297524 88.49 88.03 91.20 0.20 0.25 0.15 0.34 0.38 0.18
FUT6 ENST00000318336 88.50 98.56 96.37 0.20 0.20 0.07 0.34 0.15 0.09
OR2G3 ENST00000320002 88.50 78.12 86.50 0.20 0.43 0.30 0.34 0.74 0.33
ZSCAN4 ENST00000318203 88.51 83.22 88.97 0.20 0.28 0.19 0.34 0.47 0.28
OR6K3 ENST00000368145 88.51 93.26 93.65 0.20 0.28 0.11 0.34 0.30 0.15
C4orf19 ENST00000284437 88.52 88.50 91.41 0.20 0.23 0.15 0.34 0.36 0.18
ZNF30 ENST00000439785 88.52 88.52 91.43 0.20 0.23 0.15 0.34 0.36 0.18
CLDN23 ENST00000519106 88.53 86.91 90.79 0.20 0.22 0.15 0.34 0.41 0.20
AKR1C3 ENST00000380554 88.53 94.36 94.18 0.20 0.23 0.09 0.34 0.24 0.12
RBMXL3 ENST00000424776 88.54 98.31 96.27 0.20 0.21 0.07 0.34 0.14 0.09
SPINK9 ENST00000377906 88.54 84.43 89.64 0.20 0.29 0.18 0.34 0.44 0.23
CD1D ENST00000368171 88.55 55.27 74.81 0.20 0.57 0.39 0.34 1.62 0.65
IGLL5 ENST00000526893 88.55 97.11 95.61 0.20 0.24 0.08 0.34 0.18 0.11
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
SPATC1L ENST00000291672 88.56 89.85 91.96 0.20 0.27 0.14 0.34 0.37 0.16
COBL ENST00000265136 88.57 23.35 55.65 0.20 1.42 0.53 0.34 0.93 1.73
SIGLEC9 ENST00000440804 88.57 54.88 74.63 0.20 0.57 0.40 0.34 1.62 0.68
RP11-144F15.1 ENST00000551505 88.58 97.06 95.58 0.20 0.24 0.08 0.34 0.19 0.11

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.