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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
RPP38 ENST00000378197 79.93 84.47 85.56 0.30 0.29 0.33 0.59 0.44 0.35
GSTA3 ENST00000211122 79.94 61.03 73.25 0.30 0.54 0.43 0.59 1.39 0.79
PRRT3 ENST00000412055 79.94 35.70 57.84 0.30 0.78 0.51 0.59 1.57 1.66
MOGAT1 ENST00000446656 79.95 83.20 84.93 0.30 0.28 0.34 0.59 0.47 0.40
KIAA1586 ENST00000370733 79.95 62.33 73.91 0.30 0.53 0.40 0.59 1.33 0.70
CTCFL ENST00000423479 79.96 30.21 54.67 0.30 1.09 0.56 0.58 1.41 1.73
KRTAP10-10 ENST00000380095 79.96 80.44 83.58 0.30 0.37 0.33 0.58 0.59 0.40
ST20 ENST00000478497 79.97 88.30 87.34 0.30 0.23 0.28 0.58 0.38 0.31
PLEKHG4B ENST00000283426 79.98 63.04 74.43 0.30 0.48 0.40 0.58 1.31 0.70
AREG ENST00000395748 79.98 45.31 63.92 0.30 0.70 0.51 0.58 1.98 1.38
USP40 ENST00000450966 79.99 45.82 64.15 0.32 0.75 0.51 0.58 2.02 1.37
METTL11B ENST00000439373 79.99 62.95 74.34 0.32 0.51 0.40 0.58 1.31 0.70
C17orf74 ENST00000333870 80.00 71.23 78.86 0.32 0.53 0.39 0.59 1.07 0.52
SP8 ENST00000418710 80.00 11.47 44.21 0.32 2.11 0.62 0.59 0.56 2.04
SERPINA6 ENST00000341584 80.01 79.84 83.28 0.32 0.35 0.30 0.59 0.61 0.40
PLIN5 ENST00000381848 80.01 81.90 84.25 0.32 0.35 0.34 0.59 0.51 0.42
C16orf46 ENST00000299578 80.02 83.31 85.02 0.32 0.27 0.33 0.59 0.48 0.39
PKP3 ENST00000331563 80.02 36.51 58.32 0.32 0.80 0.49 0.59 1.64 1.64
OR6T1 ENST00000321252 80.03 76.47 81.63 0.32 0.43 0.37 0.59 0.84 0.47
MT1F ENST00000334350 80.03 85.20 85.90 0.32 0.25 0.33 0.59 0.45 0.33
TMEM89 ENST00000330862 80.04 32.95 56.27 0.32 0.82 0.49 0.59 1.46 1.75
MALL ENST00000272462 80.04 77.40 82.10 0.32 0.42 0.35 0.59 0.76 0.46
ARSE ENST00000381134 80.05 27.33 53.11 0.32 1.27 0.61 0.59 1.16 1.87
WBSCR28 ENST00000320531 80.05 83.87 85.32 0.32 0.28 0.34 0.59 0.46 0.36
HS3ST6 ENST00000443547 80.06 48.80 66.09 0.32 0.63 0.51 0.59 2.02 1.22

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