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
FNIP1 ENST00000510461 15.50 6.21 8.22 1.54 2.73 2.58 0.76 0.35 0.37
RBM14 ENST00000310137 15.51 5.92 8.07 1.56 2.82 2.59 0.76 0.35 0.37
RPL4 ENST00000307961 15.51 1.79 5.91 1.56 3.80 3.29 0.76 0.26 0.29
VDAC2 ENST00000313132 15.52 24.00 17.66 1.56 1.38 1.66 0.76 0.96 0.78
SFMBT1 ENST00000394752 15.52 13.71 12.18 1.56 2.06 2.29 0.76 0.59 0.49
PURG ENST00000475541 15.53 11.62 11.24 1.56 2.09 2.15 0.76 0.57 0.45
CWF19L1 ENST00000354105 15.53 64.06 38.08 1.56 0.49 0.86 0.76 1.21 2.02
HOXA5 ENST00000222726 15.54 67.64 39.93 1.56 0.53 0.81 0.76 1.19 2.01
SND1 ENST00000354725 15.54 10.50 10.62 1.56 2.20 2.16 0.76 0.50 0.43
SKIV2L2 ENST00000230640 15.55 13.04 11.88 1.56 2.07 2.25 0.76 0.59 0.46
BRWD1 ENST00000333229 15.55 6.66 8.48 1.56 2.66 2.51 0.76 0.37 0.37
RAP1GAP ENST00000290101 15.56 15.76 13.28 1.56 1.89 2.06 0.76 0.69 0.54
CAPRIN1 ENST00000341394 15.56 13.76 12.24 1.56 2.06 2.26 0.76 0.59 0.50
C19orf43 ENST00000242784 15.57 47.80 29.86 1.56 0.59 0.86 0.76 1.99 1.44
NDST1 ENST00000261797 15.57 5.27 7.77 1.57 3.13 2.66 0.76 0.32 0.33
HERC1 ENST00000443617 15.58 7.21 8.73 1.57 2.59 2.49 0.76 0.37 0.37
MAGI2 ENST00000354212 15.58 8.36 9.43 1.57 2.52 2.29 0.76 0.46 0.40
NFE2L2 ENST00000397062 15.59 34.74 23.24 1.57 0.77 1.19 0.76 1.54 1.01
OGFRL1 ENST00000370435 15.59 39.46 25.59 1.57 0.70 1.05 0.76 1.64 1.20
CCNYL1 ENST00000339882 15.60 18.78 14.99 1.57 1.53 1.89 0.76 0.74 0.63
PRKD2 ENST00000433867 15.60 5.54 7.96 1.57 2.99 2.58 0.76 0.33 0.36
IDH2 ENST00000330062 15.61 18.23 14.66 1.57 1.49 1.97 0.76 0.74 0.59
AK1 ENST00000373176 15.61 50.00 31.02 1.57 0.66 0.82 0.76 2.01 1.52
ERC2 ENST00000288221 15.62 12.22 11.59 1.56 2.07 2.21 0.76 0.58 0.45
SP2 ENST00000376741 15.62 2.74 6.53 1.57 3.53 3.02 0.76 0.29 0.32

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.