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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
TAS2R16 ENST00000249284 88.84 99.52 96.98 0.19 0.16 0.08 0.32 0.13 0.07
GOLGA6D ENST00000434739 88.85 96.70 95.55 0.19 0.23 0.08 0.32 0.19 0.11
PTCHD3 ENST00000438700 88.85 62.62 79.06 0.19 0.51 0.39 0.32 1.30 0.53
C17orf80 ENST00000359042 88.86 58.18 76.60 0.19 0.54 0.37 0.32 1.46 0.61
EQTN ENST00000380032 88.86 91.40 92.88 0.19 0.23 0.14 0.32 0.33 0.15
OR2T35 ENST00000317450 88.87 77.22 86.27 0.19 0.43 0.33 0.32 0.78 0.33
ANKRD30A ENST00000361713 88.87 70.16 82.88 0.19 0.53 0.32 0.32 1.12 0.40
CCDC27 ENST00000294600 88.88 77.09 86.22 0.19 0.42 0.33 0.32 0.78 0.33
GYG2 ENST00000381163 88.88 82.65 88.89 0.19 0.34 0.19 0.32 0.50 0.28
IFI44L ENST00000370751 88.89 80.79 87.99 0.19 0.35 0.24 0.32 0.57 0.31
ZNF705G ENST00000400156 88.90 95.49 94.94 0.19 0.23 0.09 0.32 0.21 0.11
GLYAT ENST00000344743 88.90 86.93 90.94 0.19 0.22 0.15 0.32 0.40 0.20
WASH4P ENST00000326592 88.91 69.50 82.59 0.19 0.54 0.32 0.32 1.12 0.43
ZNF625 ENST00000439556 88.91 36.49 63.98 0.19 0.81 0.52 0.32 1.64 1.38
CPXCR1 ENST00000276127 88.92 97.70 96.08 0.19 0.21 0.07 0.32 0.18 0.11
C14orf183 ENST00000305273 88.92 81.81 88.50 0.19 0.35 0.22 0.32 0.51 0.29
ASMT ENST00000381241 88.93 96.25 95.30 0.19 0.22 0.08 0.32 0.19 0.10
ZNF678 ENST00000343776 88.93 95.50 94.96 0.19 0.23 0.09 0.32 0.21 0.10
OR4C46 ENST00000328188 88.94 97.46 95.94 0.19 0.22 0.07 0.32 0.19 0.10
ZNF700 ENST00000254321 88.94 85.63 90.34 0.19 0.27 0.15 0.32 0.44 0.21
OR5A2 ENST00000302040 88.95 97.84 96.17 0.19 0.21 0.07 0.32 0.17 0.10
TNFRSF18 ENST00000328596 88.95 92.46 93.46 0.19 0.27 0.11 0.32 0.30 0.15
SAA2 ENST00000526900 88.96 96.37 95.41 0.19 0.22 0.08 0.32 0.19 0.11
RP11-830F9.6 ENST00000378347 88.96 90.62 92.52 0.19 0.25 0.14 0.32 0.37 0.15
INSL3 ENST00000379695 88.97 82.14 88.69 0.19 0.34 0.20 0.32 0.51 0.28

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