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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
KXD1 ENST00000602094 42.75 66.00 53.80 0.78 0.54 0.62 1.77 1.22 1.79
NUDT10 ENST00000376006 42.75 66.16 53.91 0.77 0.53 0.61 1.77 1.20 1.77
ATG2A ENST00000377264 42.76 15.48 27.26 0.77 1.87 0.99 1.77 0.67 1.25
KIF26B ENST00000407071 42.76 6.60 22.80 0.78 2.63 1.19 1.77 0.37 0.98
PNLDC1 ENST00000610273 42.77 53.33 46.77 0.78 0.66 0.67 1.77 1.71 1.87
HIST1H2AL ENST00000357320 42.77 94.49 71.04 0.78 0.23 0.43 1.77 0.24 0.86
TDP1 ENST00000335725 42.78 57.52 49.05 0.78 0.56 0.72 1.77 1.48 1.83
CTNNAL1 ENST00000325551 42.78 42.99 41.10 0.78 0.62 0.76 1.77 1.89 2.06
GPR55 ENST00000392040 42.79 86.79 66.45 0.78 0.23 0.51 1.77 0.40 1.22
ECD ENST00000430082 42.79 52.90 46.51 0.78 0.65 0.66 1.77 1.80 1.90
CHMP2A ENST00000600118 42.80 42.70 40.97 0.78 0.61 0.76 1.77 1.92 2.05
KIAA1467 ENST00000197268 42.80 26.22 32.70 0.78 1.19 0.86 1.77 1.08 1.63
WNK4 ENST00000246914 42.81 57.09 48.85 0.78 0.56 0.70 1.77 1.51 1.85
GIGYF1 ENST00000275732 42.81 25.65 32.43 0.78 1.24 0.91 1.77 1.05 1.61
UTRN ENST00000367545 42.82 20.41 29.79 0.78 1.43 0.86 1.78 0.76 1.43
SYT6 ENST00000609117 42.82 44.99 42.18 0.78 0.68 0.68 1.78 1.97 2.01
ZNF76 ENST00000373953 42.83 72.95 57.92 0.78 0.51 0.48 1.77 1.03 1.66
OR51E1 ENST00000396952 42.83 86.48 66.36 0.78 0.24 0.53 1.77 0.42 1.20
ECE2 ENST00000402825 42.84 54.00 47.15 0.78 0.65 0.67 1.77 1.70 1.89
DGKE ENST00000284061 42.84 36.83 38.09 0.78 0.76 0.86 1.77 1.66 2.02
PTPRS ENST00000357368 42.85 6.78 22.98 0.78 2.67 1.20 1.77 0.37 0.98
RPE65 ENST00000262340 42.85 60.37 50.65 0.78 0.53 0.66 1.77 1.41 1.85
AK2 ENST00000354858 42.86 72.25 57.50 0.78 0.51 0.52 1.77 1.03 1.65
GINS1 ENST00000262460 42.86 69.19 55.71 0.80 0.56 0.53 1.77 1.12 1.74
RASSF2 ENST00000379400 42.87 59.05 49.95 0.80 0.49 0.61 1.77 1.43 1.90

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