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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
C15orf37 ENST00000560255 95.17 99.78 99.25 0.10 0.17 0.11 0.12 0.11 0.04
SIGLEC14 ENST00000360844 95.18 50.47 75.86 0.10 0.65 0.38 0.12 1.95 0.63
AC129492.6 ENST00000399413 95.18 97.97 98.70 0.10 0.20 0.10 0.12 0.17 0.05
ZNF433 ENST00000344980 95.19 86.02 93.29 0.10 0.25 0.13 0.12 0.43 0.15
OR10D3 ENST00000318666 95.19 78.26 89.81 0.10 0.43 0.18 0.12 0.74 0.23
SP100 ENST00000340126 95.20 35.76 67.26 0.10 0.78 0.52 0.12 1.58 1.16
C1orf101 ENST00000366534 95.20 42.52 71.36 0.10 0.59 0.43 0.12 1.87 0.86
PSG3 ENST00000327495 95.21 88.71 94.68 0.10 0.25 0.09 0.12 0.35 0.11
ZNF559 ENST00000393883 95.21 90.91 95.80 0.10 0.25 0.07 0.12 0.35 0.11
MS4A6E ENST00000300182 95.22 69.67 85.76 0.10 0.53 0.33 0.12 1.12 0.33
KIR3DL3 ENST00000291860 95.22 88.95 94.81 0.10 0.25 0.09 0.11 0.35 0.11
IL12RB1 ENST00000600835 95.23 49.38 75.21 0.10 0.65 0.37 0.11 2.01 0.67
MAGEA8 ENST00000535454 95.23 98.67 99.03 0.10 0.20 0.11 0.11 0.15 0.04
OR8D1 ENST00000357821 95.24 98.77 98.88 0.10 0.16 0.10 0.11 0.14 0.04
CST4 ENST00000217423 95.24 96.03 98.06 0.10 0.23 0.09 0.11 0.20 0.05
ZNF812 ENST00000457674 95.25 96.75 98.31 0.10 0.23 0.09 0.11 0.19 0.05
MS4A8 ENST00000300226 95.25 77.31 89.39 0.10 0.42 0.18 0.11 0.77 0.24
NUTM2F ENST00000253262 95.26 67.66 84.83 0.10 0.53 0.34 0.11 1.19 0.40
BIRC8 ENST00000426466 95.26 99.16 99.12 0.10 0.15 0.11 0.11 0.14 0.04
ZNF844 ENST00000439326 95.27 89.91 95.32 0.10 0.25 0.08 0.11 0.37 0.10
TEX40 ENST00000328404 95.27 49.65 75.39 0.10 0.66 0.37 0.11 2.02 0.65
NUTM2G ENST00000372322 95.28 67.99 84.98 0.10 0.52 0.33 0.11 1.19 0.39
C6orf222 ENST00000437635 95.28 72.86 87.24 0.10 0.49 0.28 0.11 1.05 0.31
MS4A12 ENST00000016913 95.29 88.31 94.54 0.10 0.23 0.10 0.11 0.37 0.12
TCP10L ENST00000300258 95.29 64.89 83.45 0.10 0.48 0.33 0.11 1.24 0.40

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