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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
MVB12B ENST00000361171 18.21 25.19 19.73 1.51 1.32 1.52 0.90 1.02 0.85
RBM14-RBM4 ENST00000412278 18.22 8.03 10.73 1.51 2.53 2.19 0.90 0.44 0.43
LPPR5 ENST00000263177 18.22 35.01 24.67 1.51 0.75 1.05 0.90 1.57 1.10
KPTN ENST00000338134 18.23 40.53 27.51 1.51 0.63 0.97 0.90 1.77 1.27
KDM3A ENST00000409556 18.23 7.35 10.37 1.51 2.56 2.19 0.90 0.37 0.43
BOLL ENST00000321801 18.24 29.97 22.27 1.51 1.09 1.16 0.90 1.41 0.96
DMAP1 ENST00000372289 18.24 32.46 23.45 1.51 0.86 1.19 0.90 1.48 1.00
REV3L ENST00000358835 18.25 1.37 7.17 1.51 3.96 2.86 0.90 0.27 0.34
SLC39A9 ENST00000336643 18.25 26.07 20.23 1.51 1.20 1.48 0.90 1.09 0.88
CHST1 ENST00000308064 18.26 25.12 19.71 1.51 1.32 1.53 0.90 1.03 0.85
RPL18 ENST00000549920 18.26 11.87 12.64 1.51 2.10 2.19 0.90 0.58 0.52
CTSK ENST00000271651 18.27 52.26 33.40 1.51 0.62 0.87 0.90 1.84 1.72
STOML2 ENST00000356493 18.27 36.45 25.43 1.51 0.82 1.04 0.90 1.64 1.18
ST3GAL3 ENST00000262915 18.28 33.20 23.81 1.51 0.82 1.10 0.90 1.50 1.03
SLC6A15 ENST00000266682 18.28 31.27 22.94 1.51 0.99 1.19 0.90 1.38 0.98
ANK3 ENST00000280772 18.29 0.81 6.92 1.51 4.10 2.90 0.90 0.28 0.33
SPIN4 ENST00000335144 18.29 33.90 24.11 1.51 0.84 1.10 0.90 1.55 1.06
XPOT ENST00000332707 18.30 10.85 12.15 1.51 2.14 2.29 0.90 0.50 0.49
SIX6 ENST00000327720 18.30 29.61 22.05 1.51 1.10 1.15 0.90 1.39 0.96
HIST1H2BN ENST00000396980 18.31 96.14 57.13 1.51 0.21 0.52 0.90 0.20 1.70
NTRK3 ENST00000360948 18.32 7.68 10.60 1.51 2.52 2.16 0.90 0.42 0.44
SLIT2 ENST00000504154 18.32 2.07 7.55 1.51 3.71 2.75 0.90 0.29 0.33
SLC38A1 ENST00000398637 18.33 15.30 14.52 1.51 1.90 1.99 0.90 0.67 0.59
CLP1 ENST00000533682 18.33 32.10 23.30 1.51 0.91 1.19 0.90 1.46 1.00
FBXL5 ENST00000341285 18.34 8.24 10.91 1.51 2.57 2.21 0.90 0.45 0.44

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