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
LRP2 ENST00000263816 33.32 8.35 18.84 0.92 2.51 1.56 1.70 0.46 0.83
GNB5 ENST00000261837 33.32 53.71 41.74 0.92 0.63 0.72 1.70 1.70 2.00
CDC37L1 ENST00000381854 33.33 13.89 21.73 0.92 2.05 1.25 1.70 0.60 0.93
BMX ENST00000357607 33.34 29.92 29.84 0.92 1.11 0.87 1.70 1.41 1.43
NPR1 ENST00000368680 33.34 23.39 26.47 0.92 1.42 1.00 1.70 0.93 1.25
MYLK ENST00000360304 33.35 25.54 27.57 0.92 1.25 0.96 1.70 1.05 1.26
SLC31A2 ENST00000259392 33.35 89.37 62.15 0.92 0.27 0.48 1.70 0.37 1.44
DAXX ENST00000374542 33.36 25.11 27.36 0.92 1.32 0.96 1.70 1.03 1.26
ATM ENST00000278616 33.36 36.54 33.10 0.92 0.78 0.87 1.70 1.63 1.67
OSGEP ENST00000206542 33.37 59.07 44.86 0.92 0.49 0.68 1.70 1.44 2.04
CCDC43 ENST00000315286 33.37 53.90 41.84 0.92 0.65 0.68 1.71 1.70 2.02
DTX4 ENST00000227451 33.38 20.88 25.21 0.92 1.42 1.05 1.71 0.84 1.16
ARHGEF1 ENST00000337665 33.38 14.98 22.36 0.92 1.92 1.16 1.71 0.64 0.97
RNF144B ENST00000259939 33.39 72.74 52.33 0.92 0.48 0.61 1.71 1.04 1.91
PYGO1 ENST00000302000 33.39 7.56 18.42 0.92 2.51 1.62 1.71 0.42 0.81
TESC ENST00000335209 33.40 29.73 29.74 0.92 1.11 0.86 1.70 1.40 1.42
ERLEC1 ENST00000185150 33.40 35.69 32.74 0.92 0.78 0.86 1.70 1.57 1.65
KERA ENST00000266719 33.41 79.10 55.92 0.92 0.39 0.49 1.70 0.69 1.76
ZDHHC18 ENST00000374142 33.41 43.87 36.85 0.92 0.61 0.81 1.70 1.97 1.94
KIF20A ENST00000394894 33.42 40.13 34.96 0.92 0.62 0.90 1.70 1.72 1.74
TBC1D22A ENST00000337137 33.42 20.57 25.08 0.92 1.44 1.05 1.70 0.76 1.16
PIGO ENST00000378617 33.43 44.39 37.16 0.92 0.62 0.81 1.70 1.97 1.97
CCDC106 ENST00000586790 33.43 53.50 41.70 0.92 0.65 0.72 1.70 1.71 2.01
STK17B ENST00000263955 33.44 33.86 31.85 0.92 0.84 0.92 1.70 1.55 1.57
C5 ENST00000223642 33.44 36.87 33.29 0.92 0.76 0.89 1.70 1.68 1.70

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.