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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
OR12D2 ENST00000383555 72.96 45.51 59.55 0.32 0.72 0.49 0.79 1.99 1.70
HLA-DMB ENST00000418107 72.97 52.66 64.11 0.32 0.68 0.52 0.79 1.80 1.37
MAMLD1 ENST00000432680 72.97 23.17 46.80 0.32 1.46 0.67 0.79 0.90 1.86
PRRG3 ENST00000370353 72.98 89.15 84.40 0.32 0.27 0.33 0.79 0.35 0.40
RBMXL1 ENST00000399794 72.98 53.09 64.31 0.33 0.66 0.51 0.79 1.77 1.36
DMRTB1 ENST00000371445 72.99 22.62 46.46 0.33 1.47 0.67 0.79 0.86 1.92
ENTPD6 ENST00000376652 72.99 45.03 59.20 0.33 0.68 0.49 0.79 1.97 1.68
KCNK7 ENST00000340313 73.00 85.86 82.83 0.33 0.28 0.32 0.79 0.43 0.42
SCAF1 ENST00000360565 73.00 9.52 39.62 0.33 2.51 0.78 0.79 0.49 2.04
SPA17 ENST00000532692 73.01 68.25 73.44 0.33 0.52 0.40 0.79 1.21 0.76
F7 ENST00000375581 73.01 48.27 61.31 0.33 0.63 0.44 0.79 2.00 1.48
MMP28 ENST00000250144 73.02 87.89 83.83 0.34 0.24 0.34 0.79 0.38 0.42
HLA-F ENST00000259951 73.02 50.75 62.88 0.34 0.63 0.51 0.79 1.94 1.40
FAM96B ENST00000422424 73.03 86.45 83.11 0.34 0.24 0.30 0.79 0.42 0.40
FAM186B ENST00000257894 73.03 65.28 71.71 0.34 0.51 0.46 0.79 1.24 0.82
FBXO6 ENST00000376753 73.04 50.66 62.80 0.33 0.63 0.48 0.79 1.95 1.39
SERTAD3 ENST00000322354 73.04 80.24 79.98 0.33 0.37 0.35 0.79 0.58 0.52
FAM83F ENST00000333407 73.05 78.21 78.89 0.33 0.43 0.39 0.79 0.74 0.52
GPR128 ENST00000273352 73.05 60.84 68.97 0.33 0.56 0.46 0.78 1.41 1.04
DAPL1 ENST00000309950 73.06 93.22 86.35 0.33 0.28 0.33 0.78 0.30 0.33
RP11-1055B8.7 ENST00000307745 73.06 3.99 36.67 0.33 3.27 0.84 0.78 0.32 1.93
AKR7L ENST00000420396 73.07 82.50 81.14 0.33 0.34 0.39 0.78 0.52 0.49
WDR52 ENST00000393845 73.07 29.15 50.13 0.33 1.13 0.63 0.78 1.34 1.90
OR52E2 ENST00000321522 73.08 69.98 74.44 0.33 0.53 0.40 0.78 1.14 0.69
ZNF738 ENST00000311015 73.09 64.59 71.31 0.33 0.48 0.43 0.78 1.22 0.87

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