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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
CACNB1 ENST00000394303 27.12 17.67 20.49 1.25 1.56 1.49 1.38 0.73 0.89
TTI1 ENST00000373448 27.13 42.39 32.92 1.25 0.59 0.86 1.38 1.90 1.66
KLHL41 ENST00000284669 27.13 42.13 32.81 1.25 0.61 0.86 1.39 1.86 1.65
GON4L ENST00000437809 27.14 11.64 17.26 1.25 2.09 1.64 1.39 0.57 0.74
ATXN2 ENST00000377617 27.14 13.70 18.36 1.25 2.06 1.66 1.39 0.59 0.80
ISLR2 ENST00000361742 27.15 30.78 27.12 1.25 1.06 0.99 1.39 1.38 1.26
TEX30 ENST00000376032 27.15 72.09 48.52 1.25 0.52 0.68 1.39 1.04 1.86
ST8SIA1 ENST00000396037 27.16 26.61 24.93 1.25 1.20 1.02 1.39 1.12 1.12
PLCD3 ENST00000322765 27.16 40.66 32.10 1.25 0.63 0.90 1.39 1.77 1.60
GALNT13 ENST00000392825 27.17 11.30 17.10 1.25 2.13 1.66 1.39 0.55 0.73
IGFBP2 ENST00000233809 27.17 47.01 35.29 1.25 0.68 0.86 1.39 1.98 1.75
TPD52 ENST00000379097 27.18 69.27 46.98 1.25 0.57 0.70 1.39 1.14 1.87
SS18L2 ENST00000447630 27.18 82.77 54.54 1.24 0.33 0.56 1.40 0.50 1.75
PFDN2 ENST00000368010 27.19 36.52 30.03 1.24 0.80 0.81 1.40 1.63 1.46
SH3PXD2A ENST00000355946 27.19 10.08 16.46 1.24 2.34 1.71 1.40 0.49 0.69
FLCN ENST00000285071 27.20 15.91 19.58 1.24 1.89 1.53 1.40 0.68 0.85
PHKA1 ENST00000373542 27.20 28.72 26.13 1.24 1.15 0.99 1.40 1.29 1.27
ADAMTSL2 ENST00000354484 27.21 39.86 31.73 1.24 0.65 0.89 1.40 1.69 1.59
TNFRSF11B ENST00000297350 27.21 26.74 25.04 1.23 1.21 1.04 1.40 1.12 1.15
FBXL4 ENST00000369244 27.22 53.31 38.57 1.23 0.66 0.84 1.41 1.72 2.01
TGM2 ENST00000361475 27.22 65.53 45.03 1.23 0.53 0.70 1.40 1.22 2.04
ZAP70 ENST00000264972 27.23 18.90 21.19 1.23 1.52 1.40 1.40 0.76 0.90
NAF1 ENST00000274054 27.24 12.82 17.93 1.23 2.09 1.68 1.40 0.59 0.77
PRICKLE1 ENST00000455697 27.24 2.12 12.27 1.23 3.68 2.25 1.40 0.28 0.50
SCRN1 ENST00000434476 27.25 35.99 29.80 1.23 0.80 0.85 1.40 1.59 1.43

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