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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
PLA2G2E ENST00000375116 59.66 84.30 74.90 0.58 0.28 0.39 1.39 0.44 0.64
VSIG2 ENST00000326621 59.67 63.35 62.35 0.58 0.48 0.48 1.40 1.30 1.41
CHRNG ENST00000389494 59.67 74.68 69.30 0.58 0.54 0.43 1.40 0.96 0.98
OR51T1 ENST00000380378 59.68 89.09 77.60 0.58 0.27 0.37 1.41 0.35 0.56
ZNF829 ENST00000520965 59.68 67.20 64.85 0.58 0.54 0.51 1.41 1.22 1.34
C9orf84 ENST00000374287 59.69 45.79 51.93 0.58 0.75 0.62 1.41 2.02 1.93
TMEM220 ENST00000341871 59.69 85.27 75.41 0.58 0.25 0.37 1.40 0.46 0.66
ADAMTS8 ENST00000257359 59.70 50.69 54.79 0.58 0.63 0.53 1.40 1.94 1.74
TM4SF18 ENST00000296059 59.70 83.06 74.25 0.58 0.30 0.39 1.39 0.49 0.69
IMPA1 ENST00000449740 59.71 44.23 51.05 0.58 0.62 0.66 1.40 1.95 1.89
SGK494 ENST00000301037 59.71 58.09 59.06 0.58 0.53 0.49 1.40 1.46 1.66
OR8U1 ENST00000302270 59.72 94.76 80.57 0.58 0.23 0.39 1.40 0.24 0.51
CLEC9A ENST00000355819 59.72 66.22 64.27 0.58 0.53 0.51 1.40 1.20 1.35
TMBIM4 ENST00000358230 59.73 77.10 70.75 0.58 0.42 0.43 1.40 0.78 0.86
MAS1 ENST00000252660 59.73 76.95 70.64 0.58 0.43 0.43 1.40 0.79 0.90
PROM2 ENST00000317620 59.74 47.66 53.13 0.58 0.61 0.61 1.40 1.97 1.87
CFTR ENST00000003084 59.74 71.60 67.47 0.58 0.53 0.52 1.40 1.07 1.14
ZSWIM2 ENST00000295131 59.75 69.43 66.26 0.58 0.56 0.52 1.40 1.13 1.20
FPGT-TNNI3K ENST00000557284 59.75 76.24 70.23 0.58 0.43 0.43 1.40 0.85 0.91
APOD ENST00000343267 59.76 73.35 68.55 0.59 0.54 0.47 1.40 1.02 1.06
DNAJC28 ENST00000314399 59.76 74.98 69.55 0.59 0.53 0.44 1.40 0.93 0.96
CDC42BPG ENST00000342711 59.77 43.29 50.56 0.59 0.61 0.67 1.40 1.94 1.86
ARL2 ENST00000246747 59.77 57.69 58.82 0.59 0.56 0.51 1.40 1.48 1.65
DDIT4L ENST00000273990 59.78 91.40 78.82 0.59 0.23 0.39 1.39 0.33 0.52
FAM114A2 ENST00000351797 59.79 55.29 57.46 0.59 0.57 0.51 1.39 1.62 1.66

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