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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
CD151 ENST00000397420 40.16 57.92 47.90 0.86 0.57 0.66 1.74 1.46 1.89
RCAN1 ENST00000313806 40.17 59.84 48.90 0.86 0.52 0.71 1.74 1.36 1.84
TMEM180 ENST00000238936 40.17 31.05 33.77 0.86 1.04 0.89 1.74 1.35 1.74
RIPK4 ENST00000332512 40.18 29.63 33.07 0.86 1.10 0.86 1.74 1.39 1.66
TNC ENST00000350763 40.18 20.94 28.70 0.86 1.43 0.80 1.75 0.83 1.34
EAF1 ENST00000396842 40.19 40.86 38.80 0.86 0.61 0.82 1.75 1.78 2.03
KLC4 ENST00000259708 40.19 27.61 32.09 0.86 1.27 0.90 1.74 1.17 1.60
TCTN3 ENST00000371217 40.20 58.75 48.33 0.86 0.54 0.67 1.74 1.43 1.88
RFC1 ENST00000381897 40.20 12.88 24.60 0.86 2.07 1.06 1.74 0.59 1.10
SLC25A43 ENST00000217909 40.21 49.91 43.43 0.86 0.66 0.63 1.74 2.02 2.01
ACADM ENST00000420607 40.21 63.87 51.14 0.86 0.49 0.65 1.74 1.21 1.90
GHRHR ENST00000326139 40.22 51.74 44.51 0.86 0.61 0.61 1.73 1.88 2.04
STARD3 ENST00000336308 40.23 35.39 35.92 0.86 0.77 0.86 1.73 1.56 1.79
LXN ENST00000264265 40.23 74.32 57.17 0.86 0.53 0.52 1.73 1.01 1.69
ACADL ENST00000233710 40.24 63.36 50.90 0.86 0.48 0.66 1.73 1.30 1.85
WNT16 ENST00000222462 40.24 64.53 51.53 0.86 0.47 0.62 1.73 1.22 1.92
ALOX12B ENST00000319144 40.25 27.99 32.32 0.86 1.20 0.90 1.73 1.19 1.61
ADAMTS12 ENST00000504830 40.25 34.91 35.71 0.86 0.76 0.85 1.73 1.55 1.76
CHST9 ENST00000284224 40.26 62.79 50.55 0.86 0.51 0.67 1.73 1.31 1.86
KLHL4 ENST00000373114 40.26 22.41 29.52 0.86 1.51 0.84 1.73 0.82 1.38
MPHOSPH8 ENST00000361479 40.27 24.54 30.64 0.86 1.30 0.80 1.73 1.03 1.47
RBM24 ENST00000379052 40.27 38.72 37.71 0.86 0.70 0.84 1.73 1.67 2.01
KCTD20 ENST00000373731 40.28 43.54 40.21 0.86 0.61 0.82 1.73 1.96 2.00
MCM6 ENST00000264156 40.28 13.35 24.84 0.86 2.05 1.02 1.73 0.61 1.10
TMEM100 ENST00000575734 40.29 67.63 53.36 0.86 0.53 0.62 1.73 1.19 1.85

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