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
STK25 ENST00000316586 14.47 29.20 19.89 1.56 1.13 1.47 0.73 1.35 0.84
PPP2R5B ENST00000164133 14.47 12.35 11.06 1.56 2.06 2.20 0.73 0.59 0.45
CLOCK ENST00000309964 14.48 8.50 8.86 1.56 2.52 2.47 0.73 0.46 0.38
SYP ENST00000263233 14.48 18.83 14.39 1.56 1.53 2.01 0.73 0.74 0.59
PFKM ENST00000340802 14.49 51.01 30.94 1.56 0.65 0.81 0.73 1.92 1.51
POLR2I ENST00000221859 14.49 39.51 25.07 1.56 0.70 1.05 0.73 1.63 1.16
PSME4 ENST00000404125 14.50 4.55 6.88 1.56 3.25 2.91 0.73 0.32 0.33
CADM4 ENST00000222374 14.50 3.89 6.55 1.54 3.29 3.01 0.73 0.31 0.32
ADK ENST00000286621 14.51 41.82 26.31 1.54 0.59 1.00 0.73 1.80 1.25
MYO1B ENST00000392318 14.51 20.44 15.24 1.54 1.43 1.83 0.73 0.76 0.65
ZNF143 ENST00000396602 14.52 30.10 20.38 1.54 1.08 1.49 0.73 1.41 0.88
DDX19B ENST00000288071 14.52 44.84 27.84 1.54 0.68 0.87 0.73 1.98 1.28
KAT6A ENST00000396930 14.53 0.38 4.77 1.54 4.14 3.67 0.73 0.28 0.25
GNG2 ENST00000335281 14.53 73.49 42.26 1.54 0.53 0.70 0.73 1.03 2.02
CALN1 ENST00000395275 14.54 43.18 27.03 1.54 0.62 0.99 0.73 1.91 1.29
COPS6 ENST00000303904 14.54 10.48 10.08 1.54 2.23 2.25 0.73 0.50 0.42
SIGMAR1 ENST00000277010 14.55 38.24 24.43 1.54 0.76 1.08 0.73 1.70 1.08
GTF2I ENST00000324896 14.56 8.18 8.71 1.54 2.57 2.51 0.73 0.44 0.37
EYA1 ENST00000340726 14.56 11.65 10.71 1.54 2.09 2.19 0.73 0.57 0.43
DHCR24 ENST00000371269 14.57 25.93 18.20 1.54 1.21 1.66 0.73 1.09 0.79
TBC1D23 ENST00000394144 14.57 29.46 20.10 1.54 1.09 1.49 0.73 1.39 0.85
TIMP2 ENST00000262768 14.58 24.24 17.27 1.54 1.32 1.64 0.73 0.99 0.74
WDR20 ENST00000454394 14.58 17.75 13.83 1.54 1.53 2.09 0.73 0.72 0.57
BIRC6 ENST00000421745 14.59 1.27 5.19 1.54 3.98 3.59 0.73 0.27 0.26
CTD-2116N17.1 ENST00000606793 14.59 25.17 17.78 1.56 1.32 1.66 0.73 1.02 0.78

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.