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
RBBP6 ENST00000319715 8.66 0.58 2.29 2.42 4.15 4.05 0.44 0.28 0.23
TGFB2 ENST00000366929 8.66 2.89 3.23 2.42 3.50 3.89 0.44 0.29 0.24
VDAC1 ENST00000265333 8.67 13.22 8.30 2.42 2.05 2.58 0.44 0.60 0.37
DLL4 ENST00000249749 8.67 2.57 3.05 2.42 3.55 3.95 0.44 0.29 0.24
ETV1 ENST00000430479 8.68 17.02 10.40 2.42 1.62 2.19 0.44 0.73 0.43
UPF3B ENST00000276201 8.68 7.37 5.33 2.42 2.56 3.54 0.44 0.37 0.25
PRKAG1 ENST00000316299 8.69 42.06 23.49 2.42 0.61 1.18 0.44 1.85 1.00
HIPK1 ENST00000369558 8.69 1.91 2.76 2.42 3.75 4.04 0.44 0.26 0.23
ZBTB12 ENST00000375527 8.70 13.36 8.40 2.42 2.05 2.52 0.44 0.60 0.38
MAPRE3 ENST00000233121 8.70 24.59 14.36 2.42 1.30 2.01 0.44 1.05 0.59
ILF3 ENST00000449870 8.71 1.13 2.51 2.42 4.01 4.01 0.44 0.28 0.24
TSPAN5 ENST00000305798 8.71 18.97 11.50 2.42 1.52 2.19 0.44 0.76 0.45
YME1L1 ENST00000326799 8.72 21.81 12.80 2.42 1.47 2.11 0.44 0.81 0.52
MAP4K4 ENST00000347699 8.72 4.28 3.85 2.42 3.25 3.76 0.44 0.32 0.24
UBQLN1 ENST00000376395 8.73 6.94 5.09 2.42 2.59 3.64 0.44 0.37 0.25
RAE1 ENST00000395841 8.73 5.50 4.39 2.42 3.02 3.72 0.44 0.33 0.24
GABRA4 ENST00000264318 8.74 15.97 9.90 2.40 1.87 2.30 0.44 0.68 0.41
OSBPL8 ENST00000261183 8.74 20.05 11.99 2.40 1.43 2.28 0.44 0.74 0.47
SHANK3 ENST00000262795 8.75 2.01 2.81 2.40 3.72 4.04 0.44 0.28 0.23
GRM5 ENST00000418177 8.75 9.56 6.49 2.40 2.49 3.05 0.44 0.49 0.32
EP300 ENST00000263253 8.76 0.75 2.42 2.42 4.11 4.02 0.44 0.27 0.23
ZC3H11A ENST00000545588 8.77 4.82 4.09 2.42 3.29 3.75 0.44 0.31 0.23
RGL2 ENST00000497454 8.77 22.15 13.04 2.42 1.52 2.09 0.45 0.82 0.52
FGFR2 ENST00000457416 8.78 10.29 6.89 2.42 2.26 2.90 0.45 0.49 0.33
VMP1 ENST00000262291 8.78 13.99 8.72 2.42 2.06 2.51 0.45 0.60 0.37

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.