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
KIAA1147 ENST00000536163 69.86 42.98 56.16 0.53 0.62 0.49 0.95 1.89 1.77
AGR3 ENST00000310398 69.87 97.41 86.79 0.52 0.22 0.30 0.95 0.19 0.31
ANKS3 ENST00000304283 69.87 39.34 54.10 0.51 0.70 0.59 0.95 1.64 1.75
RRP36 ENST00000244496 69.88 84.39 80.46 0.51 0.29 0.39 0.95 0.44 0.50
FAM150B ENST00000403610 69.88 77.87 77.03 0.51 0.42 0.37 0.95 0.79 0.61
CDCA5 ENST00000275517 69.89 61.74 67.67 0.51 0.57 0.52 0.95 1.37 1.13
SDR42E1 ENST00000328945 69.89 92.61 84.60 0.51 0.29 0.34 0.95 0.31 0.40
TMEM202 ENST00000341689 69.90 80.70 78.53 0.51 0.37 0.38 0.95 0.57 0.55
BTC ENST00000395743 69.90 57.10 64.94 0.51 0.56 0.51 0.95 1.50 1.33
TUBAL3 ENST00000380419 69.91 79.80 78.05 0.51 0.35 0.39 0.95 0.62 0.54
THTPA ENST00000288014 69.91 83.15 79.86 0.51 0.29 0.37 0.95 0.49 0.52
ETAA1 ENST00000272342 69.92 26.17 46.76 0.51 1.19 0.67 0.95 1.08 1.87
HOXD1 ENST00000331462 69.92 65.74 70.07 0.51 0.53 0.47 0.95 1.22 0.91
GIPC2 ENST00000370759 69.93 83.18 79.87 0.51 0.29 0.37 0.94 0.48 0.52
GRK4 ENST00000398052 69.93 61.36 67.42 0.51 0.54 0.52 0.94 1.40 1.15
VPS9D1 ENST00000389386 69.94 60.34 66.87 0.51 0.53 0.53 0.94 1.41 1.20
SLC6A18 ENST00000324642 69.94 79.07 77.70 0.51 0.39 0.38 0.94 0.70 0.55
MYCT1 ENST00000367245 69.95 72.79 74.24 0.51 0.49 0.39 0.94 1.04 0.69
FMO3 ENST00000367755 69.96 83.19 79.89 0.51 0.28 0.37 0.95 0.47 0.52
TPCN2 ENST00000294309 69.96 36.42 52.46 0.51 0.82 0.61 0.94 1.63 1.92
RNH1 ENST00000534797 69.97 63.42 68.71 0.51 0.49 0.46 0.94 1.27 1.05
NXNL1 ENST00000301944 69.97 85.34 81.01 0.51 0.25 0.39 0.94 0.45 0.50
C9orf85 ENST00000334731 69.98 87.09 81.90 0.51 0.22 0.37 0.94 0.40 0.46
AK3 ENST00000381809 69.98 75.23 75.56 0.51 0.49 0.38 0.94 0.90 0.64
HSPA1A ENST00000375651 69.99 72.24 73.90 0.51 0.51 0.40 0.94 1.04 0.70

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.