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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
PIGP ENST00000464265 69.09 73.96 74.44 0.57 0.53 0.40 0.96 1.02 0.69
PIEZO2 ENST00000503781 69.09 16.51 41.02 0.57 1.78 0.76 0.96 0.69 2.04
GKN2 ENST00000328895 69.10 74.16 74.55 0.57 0.53 0.40 0.96 1.03 0.69
TRIM58 ENST00000366481 69.10 82.12 78.85 0.57 0.34 0.39 0.97 0.50 0.52
PCDHGB3 ENST00000576222 69.11 46.04 57.53 0.57 0.77 0.52 0.96 2.04 1.66
VILL ENST00000283713 69.11 60.28 66.42 0.57 0.53 0.52 0.96 1.39 1.21
C8B ENST00000371237 69.12 71.90 73.29 0.57 0.51 0.43 0.96 1.07 0.79
OR6K6 ENST00000368144 69.12 82.18 78.93 0.57 0.34 0.39 0.96 0.52 0.52
SLC10A6 ENST00000273905 69.13 79.30 77.41 0.57 0.38 0.35 0.96 0.67 0.58
SPATA17 ENST00000366933 69.13 42.78 55.62 0.57 0.62 0.53 0.96 1.91 1.73
PCDHA7 ENST00000525929 69.14 55.29 63.36 0.57 0.57 0.48 0.96 1.62 1.36
ODAM ENST00000396094 69.14 78.10 76.71 0.57 0.43 0.34 0.96 0.74 0.61
MRM1 ENST00000250156 69.15 75.42 75.20 0.57 0.46 0.37 0.96 0.90 0.67
SLC36A3 ENST00000377713 69.15 39.76 53.91 0.57 0.65 0.61 0.96 1.66 1.77
GNG13 ENST00000248150 69.16 96.32 85.99 0.57 0.22 0.33 0.96 0.19 0.33
REEP3 ENST00000373758 69.16 32.52 49.79 0.57 0.86 0.65 0.97 1.49 1.88
ZDHHC19 ENST00000296326 69.17 43.98 56.37 0.57 0.61 0.49 0.97 1.96 1.74
FTCD ENST00000291670 69.18 68.14 71.11 0.57 0.53 0.43 0.97 1.21 0.86
POLD4 ENST00000312419 69.18 44.05 56.38 0.57 0.61 0.49 0.97 1.97 1.73
CLEC17A ENST00000417570 69.19 45.66 57.34 0.57 0.75 0.51 0.97 2.01 1.68
SRPK3 ENST00000370101 69.19 24.62 45.59 0.57 1.30 0.68 0.97 1.05 1.97
PHF21B ENST00000313237 69.20 8.31 36.98 0.57 2.53 0.78 0.97 0.45 1.94
PRKX ENST00000262848 69.20 49.93 59.99 0.57 0.66 0.48 0.97 2.02 1.63
TMEM156 ENST00000381938 69.21 84.03 79.93 0.56 0.27 0.37 0.97 0.45 0.52
EFCAB5 ENST00000394835 69.21 45.24 57.11 0.56 0.70 0.52 0.98 1.98 1.70

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