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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
GATS ENST00000436886 80.06 68.75 77.63 0.32 0.53 0.38 0.59 1.17 0.55
CCDC87 ENST00000333861 80.07 76.33 81.56 0.32 0.43 0.35 0.59 0.86 0.48
PRICKLE4 ENST00000458694 80.07 59.59 72.50 0.32 0.52 0.44 0.59 1.41 0.83
UGT3A1 ENST00000274278 80.08 77.75 82.27 0.32 0.42 0.34 0.59 0.79 0.45
C2orf68 ENST00000306336 80.08 85.88 86.22 0.32 0.28 0.33 0.58 0.43 0.33
GP1BA ENST00000329125 80.09 87.33 86.88 0.32 0.22 0.29 0.58 0.41 0.31
CCL7 ENST00000378569 80.09 93.98 90.11 0.32 0.25 0.18 0.58 0.26 0.22
RRP7A ENST00000323013 80.10 58.26 71.73 0.32 0.54 0.46 0.59 1.43 0.82
ISOC2 ENST00000085068 80.10 81.61 84.13 0.32 0.33 0.34 0.59 0.52 0.42
NPBWR2 ENST00000369768 80.11 90.84 88.62 0.32 0.25 0.22 0.59 0.35 0.28
ASPG ENST00000551177 80.11 61.75 73.75 0.32 0.57 0.42 0.59 1.37 0.71
RP11-503N18.3 ENST00000506607 80.12 69.88 78.27 0.32 0.54 0.38 0.59 1.15 0.55
BTN2A2 ENST00000356709 80.12 68.51 77.55 0.32 0.52 0.37 0.59 1.20 0.57
LBP ENST00000217407 80.13 71.58 79.18 0.32 0.53 0.38 0.59 1.07 0.54
TMEM141 ENST00000290079 80.14 79.89 83.37 0.32 0.37 0.33 0.59 0.61 0.40
GPRASP1 ENST00000537097 80.14 22.52 50.37 0.32 1.48 0.66 0.59 0.84 1.90
SSUH2 ENST00000544814 80.15 65.81 75.99 0.32 0.54 0.38 0.59 1.22 0.62
NPM2 ENST00000397940 80.15 54.29 69.36 0.32 0.62 0.43 0.59 1.69 0.98
ASB10 ENST00000420175 80.16 83.76 85.31 0.32 0.28 0.34 0.59 0.47 0.36
OR4A47 ENST00000446524 80.16 96.02 91.03 0.32 0.23 0.15 0.59 0.20 0.20
IQCF1 ENST00000310914 80.17 64.06 75.04 0.32 0.49 0.39 0.59 1.21 0.66
SCO2 ENST00000543927 80.17 88.93 87.71 0.32 0.25 0.24 0.59 0.35 0.32
TAS2R60 ENST00000332690 80.18 98.95 92.34 0.32 0.17 0.14 0.59 0.15 0.15
TEDDM1 ENST00000367565 80.18 90.12 88.33 0.32 0.25 0.22 0.59 0.38 0.30
C20orf141 ENST00000380589 80.19 86.30 86.45 0.32 0.25 0.30 0.59 0.43 0.32

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