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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
EGR4 ENST00000545030 77.09 57.49 69.46 0.34 0.56 0.44 0.72 1.48 0.98
ZNF789 ENST00000331410 77.10 67.92 75.45 0.34 0.52 0.38 0.72 1.17 0.66
C8orf22 ENST00000303202 77.10 87.38 85.61 0.34 0.23 0.32 0.72 0.41 0.35
CPNE7 ENST00000268720 77.11 75.70 79.70 0.34 0.44 0.38 0.72 0.88 0.53
KLRK1 ENST00000240618 77.11 89.81 86.65 0.34 0.27 0.30 0.72 0.37 0.33
TMEM74B ENST00000381894 77.12 74.18 78.94 0.34 0.53 0.39 0.72 1.03 0.52
C7orf34 ENST00000409607 77.12 92.91 88.16 0.34 0.29 0.23 0.72 0.30 0.30
CCDC153 ENST00000503566 77.13 73.86 78.75 0.34 0.53 0.39 0.72 1.03 0.53
TRIM73 ENST00000323819 77.13 85.84 84.86 0.34 0.28 0.34 0.72 0.43 0.40
IL18BP ENST00000404792 77.14 93.31 88.37 0.34 0.28 0.22 0.72 0.29 0.30
HIRIP3 ENST00000279392 77.14 49.60 64.76 0.34 0.66 0.49 0.72 2.02 1.32
HSD17B1 ENST00000585807 77.15 73.89 78.77 0.34 0.53 0.39 0.72 1.03 0.53
ATP4B ENST00000335288 77.16 58.83 70.24 0.34 0.54 0.43 0.72 1.41 0.91
LOXHD1 ENST00000300591 77.16 55.70 68.43 0.34 0.52 0.47 0.71 1.60 1.06
HBD ENST00000380299 77.17 95.48 89.44 0.34 0.24 0.18 0.71 0.21 0.24
KTI12 ENST00000371614 77.17 77.15 80.49 0.34 0.43 0.39 0.71 0.78 0.50
LY6G5B ENST00000375864 77.18 83.94 83.89 0.34 0.28 0.35 0.71 0.47 0.43
IL22RA2 ENST00000296980 77.18 92.26 87.82 0.34 0.25 0.24 0.71 0.30 0.32
OR4N5 ENST00000333629 77.19 79.38 81.67 0.34 0.38 0.37 0.71 0.67 0.47
SHARPIN ENST00000398712 77.19 54.61 67.80 0.34 0.58 0.51 0.71 1.66 1.12
TRMT61B ENST00000306108 77.20 58.00 69.81 0.34 0.54 0.44 0.71 1.44 0.93
OR10A7 ENST00000326258 77.20 47.79 63.72 0.34 0.59 0.49 0.71 1.99 1.39
OGFOD2 ENST00000397389 77.21 88.68 86.17 0.34 0.25 0.33 0.71 0.35 0.33
CLDND2 ENST00000291715 77.21 88.53 86.11 0.34 0.24 0.33 0.71 0.36 0.33
FBLN2 ENST00000404922 77.22 27.14 51.27 0.34 1.23 0.63 0.71 1.14 1.92

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