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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
AC079354.1 ENST00000541917 91.94 41.56 69.05 0.15 0.63 0.44 0.20 1.81 1.03
C18orf42 ENST00000434239 91.95 76.47 87.57 0.15 0.42 0.27 0.20 0.84 0.31
TTC34 ENST00000401095 91.95 83.29 90.94 0.15 0.27 0.15 0.20 0.48 0.20
SMIM2 ENST00000400419 91.96 88.07 92.15 0.15 0.24 0.14 0.20 0.38 0.16
AC115618.1 ENST00000376775 91.96 98.72 98.08 0.15 0.16 0.09 0.20 0.15 0.05
RP11-131H24.4 ENST00000557646 91.97 91.32 94.58 0.15 0.23 0.09 0.20 0.34 0.11
C10orf126 ENST00000375520 91.97 87.57 92.74 0.15 0.23 0.14 0.20 0.37 0.15
C8orf12 ENST00000284481 91.98 89.69 93.83 0.15 0.27 0.10 0.20 0.37 0.13
TCTEX1D4 ENST00000372200 91.98 82.12 90.32 0.15 0.34 0.15 0.20 0.50 0.21
AC139426.2 ENST00000435655 91.99 98.73 98.02 0.15 0.16 0.09 0.20 0.15 0.05
KBTBD11 ENST00000320248 91.99 47.46 72.60 0.15 0.65 0.46 0.20 2.02 0.81
CCDC166 ENST00000542437 92.00 85.49 91.77 0.15 0.25 0.15 0.20 0.45 0.18
LYRM9 ENST00000379103 92.00 83.64 91.00 0.15 0.27 0.15 0.20 0.47 0.20
CTD-2267D19.3 ENST00000578774 92.01 74.12 85.52 0.15 0.53 0.33 0.20 1.03 0.35
C1orf185 ENST00000371759 92.01 85.80 91.90 0.15 0.28 0.14 0.20 0.44 0.17
FBXL8 ENST00000258200 92.02 94.81 96.37 0.15 0.23 0.07 0.20 0.24 0.09
AC007405.2 ENST00000409786 92.03 98.75 97.19 0.15 0.16 0.08 0.20 0.14 0.06
RAB1A ENST00000409784 92.03 23.69 58.14 0.15 1.39 0.48 0.20 0.93 1.65
NPIPA2 ENST00000553201 92.04 98.76 98.21 0.15 0.16 0.09 0.20 0.14 0.05
NHLRC4 ENST00000424439 92.04 98.77 98.11 0.15 0.16 0.09 0.20 0.14 0.05
NBPF16 ENST00000417839 92.05 97.44 97.57 0.15 0.22 0.09 0.20 0.19 0.06
ZG16 ENST00000400752 92.05 34.20 64.71 0.15 0.84 0.49 0.20 1.55 1.33
ZNF703 ENST00000331569 92.06 38.78 67.43 0.15 0.70 0.52 0.20 1.66 1.14
C20orf187 ENST00000378252 92.06 94.92 96.53 0.15 0.23 0.07 0.20 0.23 0.07
G0S2 ENST00000367029 92.07 88.02 92.99 0.15 0.25 0.14 0.20 0.38 0.15

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