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
HES6 ENST00000272937 78.26 75.38 80.15 0.35 0.47 0.35 0.67 0.89 0.53
PADI1 ENST00000375471 78.26 64.45 74.19 0.35 0.48 0.39 0.67 1.22 0.69
FOXE1 ENST00000375123 78.27 30.24 53.67 0.35 1.09 0.62 0.67 1.41 1.80
GSE1 ENST00000253458 78.27 2.17 38.51 0.35 3.65 0.84 0.67 0.29 2.04
OR1I1 ENST00000209540 78.28 95.05 89.75 0.35 0.23 0.18 0.67 0.21 0.23
NOTO ENST00000398468 78.28 66.76 75.47 0.35 0.56 0.38 0.67 1.22 0.66
FXYD3 ENST00000604255 78.29 73.60 79.26 0.35 0.52 0.38 0.67 1.03 0.54
SLC25A52 ENST00000269205 78.29 89.47 87.07 0.35 0.27 0.28 0.67 0.36 0.30
OR4N2 ENST00000315947 78.30 89.54 87.09 0.35 0.27 0.28 0.66 0.36 0.30
TPRN ENST00000409012 78.30 41.61 60.44 0.35 0.63 0.44 0.66 1.80 1.58
C11orf16 ENST00000326053 78.31 84.44 84.73 0.35 0.29 0.34 0.66 0.44 0.40
UPK3B ENST00000419923 78.31 66.84 75.52 0.35 0.53 0.37 0.66 1.24 0.66
LYZL1 ENST00000375500 78.32 88.94 86.78 0.35 0.25 0.30 0.66 0.35 0.31
ZNF175 ENST00000262259 78.32 49.46 65.45 0.35 0.66 0.52 0.66 2.02 1.31
NECAB2 ENST00000305202 78.33 77.64 81.33 0.35 0.42 0.38 0.66 0.79 0.48
ANO9 ENST00000332826 78.33 46.97 63.92 0.35 0.71 0.51 0.66 1.95 1.38
WDR25 ENST00000335290 78.34 42.29 60.93 0.35 0.61 0.43 0.66 1.89 1.58
ACSM1 ENST00000307493 78.34 60.09 71.77 0.35 0.52 0.46 0.66 1.38 0.81
ARL13A ENST00000450049 78.35 73.03 78.99 0.35 0.51 0.39 0.66 1.03 0.53
OR2A14 ENST00000408899 78.35 85.71 85.39 0.35 0.27 0.34 0.66 0.44 0.35
FAM154B ENST00000339465 78.36 90.50 87.56 0.35 0.25 0.27 0.66 0.37 0.31
S100A8 ENST00000368733 78.36 89.13 86.93 0.35 0.27 0.29 0.66 0.35 0.31
EVC ENST00000382674 78.37 58.45 70.75 0.35 0.54 0.43 0.66 1.39 0.86
NOMO3 ENST00000399336 78.37 43.91 61.90 0.35 0.61 0.48 0.66 1.97 1.45
NINL ENST00000278886 78.38 58.29 70.65 0.35 0.54 0.43 0.66 1.43 0.90

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.