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
FLOT1 ENST00000376389 9.04 48.37 26.91 2.33 0.63 0.99 0.46 2.00 1.27
UGDH ENST00000316423 9.05 38.06 21.69 2.33 0.77 1.25 0.46 1.70 0.92
TRIP13 ENST00000166345 9.05 8.99 6.33 2.33 2.45 3.09 0.46 0.47 0.32
SIN3B ENST00000379803 9.06 3.95 3.85 2.33 3.28 3.76 0.46 0.32 0.24
SCAMP5 ENST00000361900 9.06 26.89 15.80 2.32 1.23 1.77 0.46 1.12 0.66
HIRA ENST00000263208 9.07 2.40 3.17 2.30 3.61 3.90 0.46 0.29 0.24
LHX9 ENST00000367387 9.07 10.99 7.40 2.30 2.09 2.80 0.46 0.52 0.34
ABCD2 ENST00000308666 9.08 37.26 21.26 2.30 0.76 1.39 0.46 1.66 0.90
RILPL2 ENST00000280571 9.09 53.64 29.55 2.30 0.63 0.84 0.46 1.70 1.38
PRKRA ENST00000325748 9.09 28.18 16.45 2.30 1.18 1.72 0.46 1.21 0.69
FAU ENST00000529639 9.10 23.20 13.79 2.30 1.43 2.07 0.47 0.91 0.57
GABARAP ENST00000302386 9.10 43.78 24.55 2.30 0.61 1.06 0.47 1.96 1.09
PTDSS1 ENST00000517309 9.11 22.40 13.36 2.30 1.51 2.04 0.47 0.82 0.55
RHOT1 ENST00000358365 9.11 15.73 9.98 2.30 1.87 2.25 0.46 0.69 0.42
TSC22D1 ENST00000458659 9.12 13.68 8.74 2.30 2.06 2.49 0.46 0.59 0.37
RGS7 ENST00000366565 9.12 15.20 9.64 2.30 1.89 2.26 0.46 0.67 0.40
DDX39A ENST00000242776 9.13 21.70 13.02 2.30 1.46 2.09 0.46 0.81 0.52
FBXL14 ENST00000339235 9.13 22.68 13.53 2.30 1.46 2.05 0.46 0.88 0.57
HRH3 ENST00000340177 9.14 37.57 21.49 2.30 0.80 1.30 0.46 1.68 0.91
DCTN2 ENST00000434715 9.14 8.54 6.11 2.30 2.52 3.26 0.46 0.47 0.30
ZDHHC14 ENST00000359775 9.15 16.49 10.36 2.30 1.78 2.19 0.46 0.69 0.43
ARMC8 ENST00000481646 9.15 4.00 3.92 2.29 3.26 3.76 0.46 0.32 0.23
GJC1 ENST00000426548 9.16 8.22 5.96 2.28 2.58 3.26 0.46 0.45 0.29
KDM6B ENST00000254846 9.16 2.79 3.42 2.28 3.53 3.86 0.47 0.28 0.23
PSMD2 ENST00000310118 9.17 1.16 2.65 2.28 4.01 4.00 0.47 0.28 0.23

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.