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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
CYB561A3 ENST00000426130 33.19 49.67 39.79 0.91 0.66 0.80 1.69 2.02 2.02
DPP3 ENST00000360510 33.20 44.11 36.86 0.91 0.59 0.81 1.69 1.99 1.94
VPS16 ENST00000380445 33.20 45.28 37.49 0.91 0.70 0.84 1.70 1.97 2.01
RABL5 ENST00000315322 33.21 37.64 33.58 0.91 0.78 0.87 1.70 1.71 1.72
TBC1D4 ENST00000377636 33.21 49.56 39.76 0.91 0.66 0.80 1.70 2.02 2.03
CHCHD4 ENST00000295767 33.22 55.70 42.78 0.91 0.52 0.70 1.70 1.60 2.02
B3GNT5 ENST00000326505 33.22 23.15 26.30 0.91 1.46 1.00 1.70 0.90 1.25
NEDD9 ENST00000379446 33.23 21.98 25.67 0.91 1.48 1.05 1.70 0.81 1.22
CLSTN3 ENST00000266546 33.23 12.02 20.77 0.92 2.07 1.46 1.70 0.57 0.89
C7orf55 ENST00000297534 33.24 84.38 58.93 0.92 0.29 0.49 1.70 0.44 1.65
TRPC7 ENST00000513104 33.24 27.97 28.73 0.92 1.20 0.80 1.70 1.19 1.34
ST14 ENST00000278742 33.25 17.16 23.30 0.92 1.61 1.19 1.70 0.75 1.00
FIBP ENST00000338369 33.25 57.79 43.93 0.92 0.57 0.61 1.70 1.47 2.02
SRRM4 ENST00000267260 33.26 17.16 23.31 0.92 1.61 1.19 1.70 0.75 1.00
MDN1 ENST00000369393 33.26 13.34 21.42 0.92 2.06 1.33 1.70 0.61 0.91
GRPR ENST00000380289 33.27 45.06 37.40 0.92 0.67 0.85 1.70 1.97 2.00
PIK3R2 ENST00000222254 33.27 24.93 27.24 0.91 1.32 0.99 1.70 1.07 1.24
PLEKHA8 ENST00000449726 33.28 51.76 40.68 0.91 0.61 0.81 1.71 1.89 2.04
MYLPF ENST00000322861 33.28 27.48 28.54 0.91 1.25 0.78 1.71 1.16 1.33
VPS33B ENST00000333371 33.29 54.75 42.27 0.92 0.58 0.70 1.70 1.63 2.01
DTD2 ENST00000310850 33.29 84.18 58.85 0.92 0.27 0.51 1.70 0.44 1.65
CCT8 ENST00000286788 33.30 14.71 22.12 0.92 1.99 1.16 1.70 0.62 0.97
FABP1 ENST00000295834 33.30 94.36 65.36 0.92 0.23 0.53 1.70 0.24 1.31
ANKRD49 ENST00000544612 33.31 65.94 48.49 0.92 0.54 0.68 1.70 1.23 1.86
FBP1 ENST00000415431 33.31 38.63 34.21 0.92 0.71 0.87 1.70 1.66 1.76

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