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
ABCG8 ENST00000272286 71.20 74.86 76.04 0.42 0.53 0.38 0.86 0.95 0.62
ABHD1 ENST00000316470 70.45 95.07 86.01 0.49 0.23 0.33 0.91 0.21 0.33
ABHD10 ENST00000273359 56.95 64.27 61.28 0.57 0.49 0.44 1.58 1.20 1.48
ABHD11 ENST00000222800 79.02 54.81 68.96 0.32 0.57 0.46 0.64 1.63 1.04
ABHD12 ENST00000376542 41.21 41.17 39.53 0.85 0.59 0.80 1.71 1.82 2.03
ABHD12B ENST00000337334 72.72 82.86 81.12 0.32 0.32 0.39 0.78 0.49 0.49
ABHD13 ENST00000375898 12.89 18.39 13.24 1.70 1.47 2.09 0.64 0.75 0.53
ABHD14A ENST00000273596 72.43 75.90 77.33 0.32 0.43 0.35 0.79 0.88 0.58
ABHD14A-ACY1 ENST00000463937 59.64 59.35 59.90 0.57 0.51 0.49 1.40 1.41 1.63
ABHD14B ENST00000483233 38.38 86.61 63.73 0.90 0.24 0.49 1.73 0.40 1.38
ABHD15 ENST00000307201 75.20 78.51 80.19 0.38 0.42 0.35 0.76 0.74 0.52
ABHD16A ENST00000395952 18.53 18.81 16.49 1.54 1.53 1.71 0.91 0.74 0.69
ABHD16B ENST00000369916 83.35 65.25 77.53 0.28 0.51 0.35 0.52 1.24 0.57
ABHD17A ENST00000250974 26.79 42.23 32.69 1.30 0.61 0.86 1.37 1.89 1.63
ABHD17B ENST00000377041 3.18 27.17 12.74 3.87 1.24 2.16 0.30 1.14 0.52
ABHD17C ENST00000258884 3.86 14.60 6.61 3.77 2.04 3.00 0.30 0.61 0.32
ABHD2 ENST00000352732 15.31 20.21 15.59 1.56 1.43 1.77 0.75 0.74 0.66
ABHD3 ENST00000289119 35.76 61.91 47.63 0.95 0.56 0.65 1.90 1.34 1.88
ABHD4 ENST00000428304 39.48 59.24 48.22 0.91 0.49 0.66 1.77 1.44 1.87
ABHD5 ENST00000458276 32.13 56.03 42.34 0.97 0.49 0.70 1.72 1.56 2.02
ABHD6 ENST00000478253 35.02 53.73 42.66 0.92 0.63 0.68 1.87 1.70 2.02
ABHD8 ENST00000247706 41.06 12.91 25.06 0.85 2.07 1.05 1.72 0.59 1.15
ABI1 ENST00000376142 11.69 17.43 12.13 1.68 1.59 2.28 0.59 0.74 0.48
ABI2 ENST00000261017 10.24 22.41 14.01 2.04 1.51 2.05 0.54 0.82 0.60
ABI3 ENST00000225941 74.67 47.81 62.00 0.38 0.59 0.49 0.78 1.99 1.45

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.