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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
CES4A ENST00000540947 73.12 48.85 61.71 0.33 0.63 0.46 0.78 2.03 1.46
GH1 ENST00000323322 73.85 49.48 62.53 0.35 0.66 0.48 0.81 2.03 1.39
ADAM33 ENST00000356518 74.88 49.58 63.36 0.38 0.66 0.49 0.78 2.03 1.36
TREX1 ENST00000422277 76.65 49.66 64.42 0.33 0.66 0.51 0.72 2.03 1.33
KRTDAP ENST00000338897 77.42 49.78 65.05 0.34 0.66 0.51 0.67 2.03 1.31
IL4I1 ENST00000595948 78.41 49.03 65.18 0.34 0.66 0.52 0.66 2.03 1.30
PIK3IP1 ENST00000215912 79.20 49.03 65.74 0.33 0.66 0.51 0.61 2.03 1.26
MPND ENST00000262966 79.67 49.27 66.12 0.33 0.65 0.51 0.57 2.03 1.21
KRTAP4-12 ENST00000394014 82.42 49.58 67.90 0.30 0.66 0.51 0.56 2.03 1.11
FCGR1A ENST00000369168 84.73 49.72 69.38 0.29 0.66 0.43 0.47 2.03 0.98
SPDYE4 ENST00000328794 84.86 46.32 67.39 0.28 0.73 0.52 0.46 2.03 1.15
EBI3 ENST00000221847 85.57 46.10 67.68 0.28 0.75 0.52 0.46 2.03 1.13
CCDC8 ENST00000307522 85.72 46.08 67.79 0.27 0.76 0.51 0.46 2.03 1.12
CD3E ENST00000361763 87.18 48.84 70.27 0.23 0.63 0.43 0.38 2.03 0.91
PRR26 ENST00000441152 98.35 45.97 75.08 0.10 0.76 0.39 0.10 2.03 0.67
CD46 ENST00000322875 99.88 48.85 77.58 0.12 0.63 0.37 0.14 2.03 0.56
ATP5G3 ENST00000284727 6.70 45.77 24.24 2.99 0.75 1.11 0.37 2.02 1.05
PFN2 ENST00000239940 7.29 49.25 26.37 2.91 0.66 1.00 0.38 2.02 1.26
PCYT1A ENST00000292823 11.88 45.93 27.08 1.64 0.76 0.99 0.59 2.02 1.27
C7orf41 ENST00000324453 14.06 49.69 30.07 1.63 0.66 0.81 0.72 2.02 1.46
HS3ST2 ENST00000261374 14.10 45.96 28.21 1.63 0.76 0.81 0.71 2.02 1.28
PRKAA2 ENST00000371244 17.58 49.75 31.83 1.46 0.66 0.92 0.88 2.02 1.58
ZNRD1 ENST00000332435 17.67 49.50 31.81 1.47 0.65 0.90 0.88 2.02 1.58
ZNF436 ENST00000314011 18.20 46.00 30.29 1.51 0.77 0.84 0.90 2.02 1.44
CETN2 ENST00000370277 18.34 45.73 30.22 1.51 0.75 0.81 0.90 2.02 1.44

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