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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
MYOC ENST00000037502 55.64 68.42 63.10 0.59 0.52 0.49 1.65 1.21 1.39
FAM136A ENST00000037869 43.12 87.85 67.27 0.82 0.24 0.52 1.79 0.38 1.15
OTC ENST00000039007 15.02 18.44 14.47 1.56 1.48 2.00 0.75 0.76 0.58
TTC17 ENST00000039989 19.92 7.43 11.38 1.53 2.54 2.20 1.00 0.39 0.45
HOXC8 ENST00000040584 18.55 31.99 23.39 1.54 0.92 1.19 0.91 1.48 0.99
MRI1 ENST00000040663 72.41 56.07 65.85 0.32 0.51 0.51 0.79 1.55 1.25
BOD1L1 ENST00000040738 44.11 9.22 24.73 0.71 2.47 1.05 1.77 0.47 1.10
TARBP1 ENST00000040877 75.58 43.33 59.86 0.34 0.59 0.49 0.75 1.94 1.63
RTN4R ENST00000043402 46.98 12.50 27.89 0.57 2.07 0.85 1.82 0.59 1.29
PSMA4 ENST00000044462 2.88 24.71 11.47 3.94 1.30 2.21 0.30 1.05 0.45
ZPBP ENST00000046087 27.57 41.69 32.81 1.23 0.61 0.85 1.41 1.80 1.65
LCP2 ENST00000046794 14.63 13.18 11.59 1.56 2.04 2.23 0.73 0.60 0.45
DCN ENST00000052754 28.13 29.42 26.95 1.16 1.09 0.99 1.47 1.38 1.27
TNFRSF17 ENST00000053243 83.70 92.74 91.18 0.29 0.29 0.15 0.52 0.30 0.18
MRPS10 ENST00000053468 55.22 84.23 72.42 0.61 0.27 0.44 1.69 0.44 0.83
GRN ENST00000053867 51.46 24.80 36.26 0.59 1.33 0.85 1.86 1.05 1.84
THAP3 ENST00000054650 84.05 67.17 78.86 0.30 0.54 0.39 0.48 1.22 0.52
VAMP3 ENST00000054666 70.40 72.96 74.60 0.49 0.51 0.40 0.91 1.03 0.68
UTS2 ENST00000054668 82.57 72.29 80.73 0.30 0.51 0.39 0.56 1.03 0.52
RCN1 ENST00000054950 63.36 57.74 61.19 0.59 0.57 0.43 1.24 1.46 1.49
RFC2 ENST00000055077 41.71 54.55 46.85 0.81 0.59 0.67 1.73 1.66 1.88
PPP1R3F ENST00000055335 81.55 75.26 81.79 0.30 0.49 0.37 0.59 0.90 0.47
KIAA2022 ENST00000055682 30.86 6.08 16.27 0.99 2.78 1.70 1.65 0.35 0.66
ARHGEF5 ENST00000056217 78.21 51.66 66.62 0.34 0.62 0.52 0.67 1.88 1.20
NFE2L3 ENST00000056233 84.17 71.76 81.32 0.32 0.51 0.38 0.47 1.07 0.48

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