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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
EPRS ENST00000366923 24.02 24.30 22.31 1.35 1.32 1.16 1.10 0.99 0.96
XKR4 ENST00000327381 24.03 5.27 12.22 1.34 3.13 2.26 1.10 0.32 0.50
GPD2 ENST00000310454 24.03 47.39 33.87 1.34 0.66 0.89 1.10 2.01 1.73
DNER ENST00000341772 24.04 22.02 21.17 1.34 1.48 1.40 1.10 0.81 0.90
DYNC1LI1 ENST00000273130 24.04 11.23 15.47 1.34 2.11 1.81 1.10 0.55 0.67
ITPKB ENST00000429204 24.05 2.84 11.10 1.34 3.52 2.19 1.10 0.28 0.45
UST ENST00000367463 24.05 24.22 22.29 1.34 1.32 1.16 1.10 0.99 0.96
TMEM55A ENST00000285419 24.06 47.43 33.92 1.34 0.66 0.90 1.10 2.01 1.73
MAGI3 ENST00000307546 24.06 17.88 18.98 1.34 1.52 1.54 1.10 0.72 0.83
TDRKH ENST00000368822 24.07 24.83 22.62 1.34 1.33 1.18 1.10 1.06 0.96
BMPR1B ENST00000440890 24.07 7.00 13.14 1.34 2.58 2.10 1.10 0.37 0.52
INTS5 ENST00000330574 24.08 22.43 21.38 1.34 1.51 1.34 1.10 0.82 0.91
RASAL2 ENST00000367649 24.08 14.34 17.06 1.34 2.04 1.67 1.10 0.61 0.71
LONP2 ENST00000285737 24.09 72.67 47.11 1.34 0.47 0.68 1.10 1.04 1.89
SS18 ENST00000415083 24.09 16.84 18.41 1.34 1.66 1.64 1.11 0.71 0.81
HOXC6 ENST00000243108 24.10 30.15 25.20 1.34 1.09 1.05 1.11 1.40 1.16
ESM1 ENST00000381405 24.11 47.21 33.82 1.34 0.66 0.89 1.12 2.01 1.73
WDR59 ENST00000262144 24.11 37.84 29.14 1.34 0.80 0.84 1.12 1.70 1.32
DNAJB14 ENST00000442697 24.12 16.29 18.15 1.34 1.78 1.66 1.12 0.70 0.79
FAM65A ENST00000422602 24.12 13.71 16.78 1.34 2.06 1.70 1.12 0.59 0.70
ACSL6 ENST00000379264 24.13 23.51 21.94 1.34 1.40 1.18 1.12 0.92 0.97
SLC20A1 ENST00000272542 24.13 24.63 22.57 1.34 1.30 1.16 1.12 1.05 0.96
RPL37 ENST00000274242 24.14 38.19 29.33 1.34 0.77 0.82 1.12 1.71 1.34
FAM214B ENST00000378561 24.14 20.76 20.59 1.34 1.44 1.48 1.12 0.81 0.88
HIP1 ENST00000336926 24.15 13.38 16.61 1.34 2.05 1.72 1.12 0.59 0.70

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