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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
KRT28 ENST00000306658 60.18 62.75 62.32 0.61 0.51 0.48 1.40 1.31 1.41
FAM162A ENST00000477892 60.18 80.10 72.89 0.61 0.37 0.40 1.40 0.60 0.81
TMPRSS11D ENST00000283916 60.19 50.57 54.96 0.61 0.63 0.51 1.40 1.94 1.74
TMCO4 ENST00000294543 60.19 69.61 66.57 0.61 0.52 0.52 1.40 1.10 1.20
DDX31 ENST00000372159 60.20 44.01 51.18 0.61 0.61 0.63 1.40 1.97 1.91
FAM133B ENST00000445716 60.20 51.43 55.49 0.61 0.63 0.51 1.40 1.89 1.73
RBPJL ENST00000343694 60.21 59.00 60.03 0.61 0.51 0.48 1.40 1.43 1.61
TREM2 ENST00000373113 60.21 88.70 77.67 0.61 0.25 0.39 1.39 0.35 0.55
TMEM59L ENST00000600490 60.22 47.49 53.28 0.61 0.62 0.61 1.40 2.01 1.86
CHL1 ENST00000256509 60.22 30.97 44.00 0.61 1.04 0.62 1.40 1.36 2.03
SLC35F2 ENST00000525815 60.23 52.76 56.25 0.61 0.66 0.49 1.40 1.80 1.76
CA5B ENST00000318636 60.23 66.47 64.73 0.61 0.57 0.49 1.40 1.20 1.32
TBPL2 ENST00000247219 60.24 74.83 69.76 0.61 0.53 0.44 1.40 0.95 0.93
PLP2 ENST00000376327 60.24 80.60 73.16 0.61 0.37 0.43 1.40 0.57 0.79
MEF2BNB-MEF2B ENST00000444486 60.25 51.06 55.27 0.61 0.65 0.51 1.40 1.92 1.74
ACTL7A ENST00000333999 60.26 75.51 70.10 0.61 0.44 0.46 1.39 0.90 0.90
SLC29A3 ENST00000373189 60.26 69.78 66.75 0.61 0.54 0.53 1.39 1.13 1.20
GTPBP8 ENST00000383678 60.27 80.11 72.95 0.61 0.37 0.40 1.39 0.60 0.81
RALGAPA2 ENST00000202677 60.27 28.42 42.65 0.61 1.16 0.68 1.39 1.24 2.02
KRT79 ENST00000330553 60.28 79.37 72.50 0.61 0.38 0.44 1.39 0.67 0.83
GP9 ENST00000307395 60.28 78.86 72.23 0.61 0.40 0.43 1.39 0.71 0.82
PTX3 ENST00000295927 60.29 65.97 64.41 0.61 0.56 0.51 1.39 1.23 1.34
ZFP2 ENST00000361362 60.29 86.91 76.70 0.61 0.22 0.34 1.39 0.41 0.60
DSG4 ENST00000359747 60.30 44.27 51.41 0.61 0.61 0.63 1.39 1.96 1.90
CPT1C ENST00000392518 60.30 35.80 46.78 0.61 0.78 0.67 1.39 1.59 1.87

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