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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
ARID2 ENST00000334344 6.85 1.09 1.83 2.92 4.03 4.21 0.37 0.28 0.24
CDK2 ENST00000266970 6.85 18.45 10.20 2.92 1.48 2.21 0.37 0.76 0.42
RPL34 ENST00000394668 6.86 28.44 15.47 2.92 1.15 1.81 0.37 1.24 0.67
NPC2 ENST00000555619 6.86 74.78 39.19 2.92 0.54 0.78 0.36 0.96 2.06
ATR ENST00000350721 6.87 18.11 10.05 2.92 1.53 2.26 0.36 0.74 0.42
CPEB4 ENST00000265085 6.87 12.95 7.27 2.92 2.06 2.80 0.36 0.59 0.33
AQR ENST00000156471 6.88 5.96 3.77 2.92 2.82 3.78 0.36 0.35 0.24
GATAD2B ENST00000368655 6.88 1.11 1.85 2.92 4.02 4.20 0.36 0.28 0.24
GABRA3 ENST00000370314 6.89 30.07 16.28 2.91 1.09 1.70 0.37 1.41 0.66
ENY2 ENST00000521688 6.90 21.09 11.65 2.91 1.46 2.21 0.37 0.82 0.47
FBXW2 ENST00000608872 6.90 3.46 2.66 2.91 3.40 4.02 0.37 0.29 0.23
TPP2 ENST00000376065 6.91 9.99 5.69 2.91 2.34 3.34 0.37 0.49 0.27
PHF8 ENST00000357988 6.91 7.49 4.49 2.91 2.53 3.70 0.37 0.40 0.25
ANKRD46 ENST00000520552 6.92 30.85 16.72 2.91 1.08 1.68 0.37 1.37 0.70
PACS1 ENST00000320580 6.92 3.60 2.73 2.90 3.37 4.00 0.37 0.30 0.23
BCL6 ENST00000406870 6.93 14.59 8.10 2.90 2.04 2.58 0.37 0.61 0.37
PDE8B ENST00000264917 6.93 8.37 4.91 2.90 2.52 3.68 0.37 0.46 0.25
GNA13 ENST00000439174 6.94 18.86 10.47 2.90 1.53 2.18 0.37 0.74 0.43
SNRPE ENST00000414487 6.94 17.50 9.71 2.90 1.58 2.26 0.37 0.73 0.40
USP15 ENST00000280377 6.95 6.62 4.09 2.91 2.64 3.73 0.37 0.37 0.23
MLEC ENST00000228506 6.95 27.32 14.91 2.91 1.27 1.91 0.37 1.16 0.63
DYNLL1 ENST00000392509 6.96 39.98 21.61 2.91 0.63 1.27 0.37 1.68 0.93
CLIP2 ENST00000223398 6.96 5.57 3.66 2.90 2.99 3.83 0.37 0.33 0.23
FXR2 ENST00000250113 6.97 4.94 3.41 2.90 3.26 3.87 0.37 0.32 0.23
PIP5K1A ENST00000368888 6.97 29.15 15.90 2.90 1.13 1.76 0.37 1.34 0.66

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