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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
HIST1H3G ENST00000305910 66.38 97.20 85.13 0.59 0.24 0.33 1.05 0.19 0.37
ATOX1 ENST00000524142 66.38 58.79 63.87 0.59 0.54 0.49 1.05 1.42 1.39
DCHS2 ENST00000357232 66.39 56.94 62.53 0.59 0.56 0.48 1.05 1.53 1.39
FGF11 ENST00000293829 66.39 69.42 70.14 0.59 0.56 0.46 1.05 1.12 0.90
CHRNA5 ENST00000299565 66.40 64.37 67.15 0.59 0.49 0.52 1.05 1.22 1.17
RIC3 ENST00000309737 66.40 61.50 65.49 0.59 0.54 0.52 1.05 1.40 1.29
KIAA1024 ENST00000305428 66.41 36.13 50.31 0.59 0.82 0.65 1.05 1.60 1.92
OR2B11 ENST00000318749 66.41 80.84 76.72 0.59 0.35 0.34 1.05 0.57 0.61
FBXO17 ENST00000292852 66.42 88.08 80.57 0.59 0.24 0.39 1.05 0.38 0.52
OR5M11 ENST00000528616 66.42 90.69 81.94 0.59 0.25 0.37 1.04 0.36 0.47
BET1L ENST00000382762 66.43 79.91 76.26 0.59 0.37 0.37 1.04 0.61 0.61
NT5M ENST00000389022 66.43 89.17 81.15 0.59 0.27 0.39 1.05 0.35 0.49
LIM2 ENST00000221973 66.44 71.32 71.41 0.59 0.53 0.44 1.05 1.06 0.87
FAM178B ENST00000490605 66.44 52.01 59.53 0.59 0.61 0.49 1.05 1.86 1.70
PCDHGA1 ENST00000517417 66.45 46.24 56.07 0.59 0.73 0.49 1.05 2.03 1.75
NARFL ENST00000251588 66.45 57.44 63.00 0.59 0.56 0.51 1.05 1.48 1.39
FBXW8 ENST00000309909 66.46 70.50 70.82 0.59 0.52 0.43 1.04 1.08 0.87
FREM1 ENST00000422223 66.46 61.71 65.70 0.59 0.57 0.51 1.04 1.38 1.27
C16orf86 ENST00000403458 66.47 58.25 63.55 0.59 0.54 0.49 1.04 1.43 1.39
OR6Y1 ENST00000302617 66.47 81.13 76.94 0.59 0.35 0.37 1.04 0.55 0.60
DUSP27 ENST00000361200 66.48 61.95 65.80 0.59 0.56 0.51 1.03 1.36 1.25
SPIRE2 ENST00000378247 66.48 47.32 56.71 0.59 0.67 0.52 1.03 2.01 1.71
ZKSCAN7 ENST00000273320 66.49 38.14 51.43 0.59 0.77 0.63 1.03 1.72 1.91
OR52B2 ENST00000530810 66.49 95.68 84.42 0.59 0.23 0.33 1.03 0.20 0.40
FAM107B ENST00000181796 66.50 76.20 74.21 0.59 0.43 0.39 1.03 0.85 0.69

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