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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
HAS3 ENST00000306560 9.17 17.75 11.11 2.28 1.53 2.19 0.47 0.72 0.45
SENP1 ENST00000004980 9.18 9.25 6.56 2.28 2.47 3.01 0.47 0.47 0.32
PRPSAP2 ENST00000268835 9.18 41.80 23.59 2.28 0.61 1.19 0.47 1.78 1.02
TRAM1 ENST00000262213 9.19 16.20 10.25 2.29 1.81 2.21 0.47 0.70 0.42
TLN1 ENST00000314888 9.19 1.86 2.91 2.29 3.76 4.00 0.47 0.26 0.23
SARS ENST00000234677 9.20 6.72 5.22 2.29 2.67 3.56 0.47 0.37 0.26
SKI ENST00000378536 9.20 6.04 4.89 2.29 2.81 3.66 0.47 0.35 0.25
ADIPOR1 ENST00000340990 9.21 23.43 14.00 2.29 1.42 2.05 0.47 0.92 0.60
PHF13 ENST00000377648 9.21 9.82 6.88 2.29 2.39 2.91 0.47 0.49 0.33
PITPNB ENST00000335272 9.22 11.10 7.53 2.29 2.09 2.77 0.47 0.53 0.33
UBA52 ENST00000442744 9.22 33.69 19.45 2.30 0.84 1.53 0.47 1.56 0.84
SETD2 ENST00000409792 9.23 5.31 4.60 2.30 3.10 3.69 0.47 0.32 0.25
FZR1 ENST00000395095 9.24 3.96 3.93 2.30 3.28 3.77 0.47 0.32 0.23
RPS20 ENST00000519807 9.24 53.60 29.59 2.30 0.62 0.84 0.47 1.72 1.39
LRRTM3 ENST00000361320 9.25 12.76 8.37 2.30 2.09 2.52 0.47 0.59 0.37
EIF3G ENST00000253108 9.25 11.05 7.52 2.30 2.10 2.77 0.47 0.52 0.33
IKZF1 ENST00000439701 9.26 3.28 3.65 2.29 3.44 3.83 0.47 0.27 0.23
PAFAH1B3 ENST00000538771 9.26 52.40 29.00 2.29 0.62 0.81 0.47 1.83 1.31
SYN1 ENST00000295987 9.27 10.00 6.99 2.28 2.35 2.90 0.47 0.49 0.33
PPP1R8 ENST00000311772 9.27 8.07 5.94 2.26 2.52 3.28 0.47 0.44 0.29
RBM3 ENST00000376759 9.28 26.27 15.59 2.25 1.19 1.77 0.47 1.08 0.66
BRPF3 ENST00000357641 9.28 4.62 4.23 2.24 3.25 3.76 0.47 0.31 0.24
TBX4 ENST00000240335 9.29 21.13 12.76 2.24 1.47 2.13 0.47 0.82 0.52
RTN4RL2 ENST00000335099 9.29 19.79 12.09 2.24 1.42 2.29 0.47 0.74 0.48
DACH1 ENST00000305425 9.30 2.41 3.29 2.24 3.60 3.89 0.47 0.29 0.24

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