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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
PRICKLE2 ENST00000295902 19.24 10.88 12.63 1.57 2.11 2.20 0.95 0.50 0.52
NFKBIZ ENST00000326172 19.25 5.75 10.07 1.57 2.90 2.26 0.95 0.34 0.42
PIM1 ENST00000373509 19.26 19.73 17.37 1.57 1.43 1.64 0.95 0.74 0.75
NELFCD ENST00000602795 19.26 20.96 18.05 1.57 1.44 1.70 0.95 0.83 0.78
KCTD5 ENST00000301738 19.27 40.97 28.29 1.57 0.61 0.80 0.95 1.79 1.29
IL2RG ENST00000374202 19.27 6.46 10.44 1.57 2.62 2.18 0.95 0.37 0.43
CLIC4 ENST00000374379 19.28 63.79 39.86 1.57 0.49 0.78 0.95 1.22 2.02
DCUN1D4 ENST00000334635 19.28 30.74 23.11 1.57 1.06 1.20 0.95 1.36 1.00
NFIC ENST00000443272 19.29 27.09 21.29 1.57 1.23 1.39 0.95 1.12 0.91
DGKA ENST00000331886 19.29 15.29 15.09 1.57 1.90 1.86 0.95 0.67 0.62
ANKRD28 ENST00000399451 19.30 4.24 9.18 1.56 3.26 2.32 0.95 0.32 0.38
ERAS ENST00000338270 19.30 77.55 47.16 1.56 0.42 0.67 0.95 0.79 1.89
USP54 ENST00000339859 19.31 27.77 21.68 1.56 1.24 1.25 0.96 1.19 0.92
RNF26 ENST00000311413 19.31 29.03 22.35 1.56 1.15 1.16 0.96 1.31 0.97
FZD4 ENST00000531380 19.32 5.51 9.97 1.56 3.01 2.28 0.96 0.33 0.42
LFNG ENST00000222725 19.32 36.69 26.18 1.56 0.77 0.99 0.96 1.66 1.25
TMCC2 ENST00000358024 19.33 24.62 20.01 1.56 1.30 1.48 0.96 1.05 0.85
TENM2 ENST00000518659 19.33 4.05 9.07 1.56 3.24 2.38 0.96 0.32 0.38
SLITRK4 ENST00000381779 19.34 20.88 18.04 1.56 1.42 1.70 0.96 0.84 0.78
HNF4G ENST00000396423 19.34 28.52 22.03 1.56 1.15 1.16 0.96 1.26 0.97
RFX7 ENST00000423270 19.35 1.16 7.61 1.56 4.01 2.73 0.96 0.28 0.33
FEN1 ENST00000305885 19.35 75.75 46.22 1.56 0.43 0.67 0.96 0.88 1.93
ARMCX3 ENST00000341189 19.36 47.04 31.43 1.56 0.68 0.87 0.96 1.98 1.56
SLCO3A1 ENST00000318445 19.36 21.52 18.37 1.56 1.42 1.64 0.97 0.81 0.81
RBM47 ENST00000381793 19.37 6.72 10.66 1.56 2.67 2.18 0.98 0.37 0.43

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