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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
ANKDD1A ENST00000380230 69.47 70.63 72.78 0.53 0.51 0.43 0.97 1.09 0.81
PKMYT1 ENST00000262300 69.48 27.75 47.37 0.53 1.25 0.65 0.97 1.19 1.85
MRFAP1 ENST00000320912 69.49 64.47 69.05 0.53 0.48 0.44 0.98 1.22 1.03
ADRA1D ENST00000379453 69.49 71.55 73.31 0.53 0.53 0.43 0.98 1.07 0.79
PIGG ENST00000453061 69.50 53.88 62.57 0.53 0.63 0.48 0.98 1.70 1.39
MST1 ENST00000449682 69.50 55.53 63.75 0.53 0.56 0.49 0.98 1.61 1.38
ACSM5 ENST00000331849 69.51 62.85 68.16 0.53 0.51 0.49 0.98 1.29 1.08
CRYGA ENST00000304502 69.51 89.06 82.69 0.53 0.27 0.32 0.98 0.35 0.42
PGBD2 ENST00000329291 69.52 81.15 78.60 0.53 0.35 0.38 0.98 0.55 0.54
HOXD9 ENST00000249499 69.52 51.46 61.10 0.53 0.63 0.43 0.98 1.89 1.53
DPEP2 ENST00000412757 69.53 69.30 72.03 0.53 0.56 0.43 0.98 1.14 0.81
OR2J1 ENST00000377171 69.53 75.49 75.46 0.53 0.44 0.38 0.98 0.90 0.66
CCDC159 ENST00000588790 69.54 45.33 57.34 0.53 0.68 0.51 0.98 1.98 1.68
MPV17L2 ENST00000599612 69.54 77.07 76.40 0.53 0.42 0.37 0.98 0.78 0.61
TBC1D17 ENST00000221543 69.55 68.67 71.66 0.54 0.53 0.44 0.98 1.17 0.83
CTF1 ENST00000279804 69.55 89.68 82.96 0.54 0.27 0.32 0.98 0.36 0.40
TAS1R2 ENST00000375371 69.56 73.32 74.30 0.54 0.56 0.39 0.97 1.02 0.70
APOE ENST00000252486 69.56 58.11 65.35 0.54 0.53 0.53 0.97 1.46 1.32
NEK11 ENST00000383366 69.57 67.07 70.62 0.54 0.54 0.43 0.97 1.23 0.90
GTF2A1L ENST00000403751 69.57 71.81 73.48 0.54 0.51 0.40 0.96 1.07 0.76
AMZ2 ENST00000359904 69.58 79.57 77.77 0.54 0.38 0.38 0.96 0.66 0.55
TMEM196 ENST00000405764 69.58 88.84 82.61 0.54 0.25 0.32 0.96 0.35 0.43
EEF1D ENST00000423316 69.59 41.95 55.41 0.54 0.61 0.49 0.96 1.83 1.71
PGF ENST00000555567 69.59 42.16 55.54 0.54 0.62 0.52 0.97 1.86 1.74
LEPREL4 ENST00000355468 69.60 66.87 70.55 0.54 0.53 0.43 0.97 1.24 0.91

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