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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
AL079342.1 ENST00000369474 92.12 98.81 98.71 0.15 0.16 0.10 0.19 0.14 0.05
PSG1 ENST00000244296 95.78 97.49 98.70 0.11 0.22 0.10 0.11 0.19 0.05
AC129492.6 ENST00000399413 95.18 97.97 98.70 0.10 0.20 0.10 0.12 0.17 0.05
MTRNR2L9 ENST00000544932 94.07 99.86 98.69 0.11 0.17 0.10 0.13 0.11 0.05
ZNF701 ENST00000540331 97.44 95.78 98.69 0.10 0.22 0.10 0.11 0.20 0.05
C9orf163 ENST00000354376 95.46 99.35 98.68 0.11 0.16 0.10 0.11 0.12 0.05
AL136531.1 ENST00000537552 94.12 99.90 98.68 0.10 0.17 0.10 0.13 0.11 0.05
RP11-321M21.3 ENST00000578340 97.19 95.98 98.67 0.10 0.22 0.10 0.10 0.20 0.05
C20orf166 ENST00000370527 97.83 95.31 98.67 0.11 0.24 0.10 0.11 0.21 0.05
MTRNR2L3 ENST00000543500 93.31 99.47 98.66 0.15 0.16 0.10 0.15 0.13 0.05
CST9 ENST00000376971 99.16 93.94 98.66 0.11 0.25 0.10 0.12 0.26 0.05
CT62 ENST00000449977 97.36 95.71 98.65 0.10 0.23 0.10 0.11 0.20 0.05
AC023632.1 ENST00000391679 93.23 99.43 98.65 0.15 0.16 0.10 0.15 0.12 0.05
AC012493.2 ENST00000595083 93.98 99.80 98.64 0.10 0.17 0.10 0.13 0.11 0.05
CD1A ENST00000289429 96.75 96.26 98.64 0.11 0.22 0.10 0.11 0.19 0.05
DEFB112 ENST00000322246 98.93 94.06 98.63 0.10 0.25 0.10 0.11 0.26 0.05
ZNF468 ENST00000595646 96.87 96.07 98.63 0.09 0.21 0.10 0.11 0.20 0.05
C9orf170 ENST00000375941 95.89 97.04 98.62 0.11 0.24 0.10 0.11 0.19 0.05
FAM27E1 ENST00000377525 93.13 99.40 98.62 0.15 0.16 0.10 0.16 0.12 0.05
PSG4 ENST00000405312 96.10 96.77 98.61 0.11 0.23 0.10 0.11 0.19 0.05
OR1M1 ENST00000429566 95.06 97.71 98.61 0.10 0.21 0.10 0.12 0.18 0.05
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
CLPSL1 ENST00000373861 97.22 95.64 98.60 0.10 0.23 0.10 0.11 0.21 0.05
PSG8 ENST00000306511 95.89 96.93 98.59 0.11 0.24 0.10 0.11 0.19 0.05
FAM24B ENST00000368898 98.91 93.93 98.58 0.10 0.25 0.10 0.11 0.26 0.05

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