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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
AL391152.1 ENST00000391612 92.92 99.30 98.53 0.16 0.16 0.10 0.16 0.12 0.05
TMEM105 ENST00000332900 96.71 95.91 98.53 0.11 0.22 0.10 0.11 0.20 0.05
RP11-342M21.2 ENST00000558463 93.88 99.76 98.54 0.11 0.17 0.10 0.13 0.11 0.05
C9orf38 ENST00000355513 93.21 99.42 98.54 0.15 0.16 0.10 0.16 0.12 0.05
TMEM78 ENST00000323223 92.97 99.33 98.55 0.16 0.16 0.10 0.16 0.12 0.05
RFPL3 ENST00000249007 96.79 95.96 98.55 0.11 0.22 0.10 0.11 0.20 0.05
GVQW1 ENST00000451672 89.91 97.69 98.56 0.18 0.21 0.10 0.28 0.19 0.05
PRAMEF1 ENST00000332296 98.16 94.61 98.56 0.11 0.23 0.10 0.11 0.24 0.05
CST9L ENST00000376979 95.43 97.33 98.57 0.11 0.23 0.10 0.11 0.19 0.05
KRTAP12-2 ENST00000360770 94.70 97.96 98.57 0.10 0.20 0.10 0.11 0.17 0.05
PNMA5 ENST00000439251 95.01 98.00 98.58 0.10 0.20 0.10 0.12 0.17 0.05
FAM24B ENST00000368898 98.91 93.93 98.58 0.10 0.25 0.10 0.11 0.26 0.05
PSG8 ENST00000306511 95.89 96.93 98.59 0.11 0.24 0.10 0.11 0.19 0.05
CLPSL1 ENST00000373861 97.22 95.64 98.60 0.10 0.23 0.10 0.11 0.21 0.05
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
OR1M1 ENST00000429566 95.06 97.71 98.61 0.10 0.21 0.10 0.12 0.18 0.05
PSG4 ENST00000405312 96.10 96.77 98.61 0.11 0.23 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
C9orf170 ENST00000375941 95.89 97.04 98.62 0.11 0.24 0.10 0.11 0.19 0.05
ZNF468 ENST00000595646 96.87 96.07 98.63 0.09 0.21 0.10 0.11 0.20 0.05
DEFB112 ENST00000322246 98.93 94.06 98.63 0.10 0.25 0.10 0.11 0.26 0.05
CD1A ENST00000289429 96.75 96.26 98.64 0.11 0.22 0.10 0.11 0.19 0.05
AC012493.2 ENST00000595083 93.98 99.80 98.64 0.10 0.17 0.10 0.13 0.11 0.05
AC023632.1 ENST00000391679 93.23 99.43 98.65 0.15 0.16 0.10 0.15 0.12 0.05
CT62 ENST00000449977 97.36 95.71 98.65 0.10 0.23 0.10 0.11 0.20 0.05

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