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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
HEATR2 ENST00000297440 82.52 50.46 68.48 0.30 0.65 0.47 0.56 1.95 1.06
WDR18 ENST00000251289 82.52 9.19 44.33 0.30 2.48 0.61 0.56 0.46 2.04
AP003068.6 ENST00000530719 82.53 91.01 89.87 0.30 0.25 0.18 0.56 0.35 0.23
C8orf76 ENST00000276704 82.53 80.45 84.86 0.30 0.37 0.34 0.56 0.59 0.40
CEP78 ENST00000376597 82.54 54.71 71.04 0.30 0.58 0.43 0.56 1.65 0.86
SCGB2B2 ENST00000601241 82.54 92.99 90.83 0.30 0.28 0.15 0.56 0.30 0.20
AKR1E2 ENST00000298375 82.55 74.87 82.09 0.30 0.53 0.35 0.56 0.95 0.46
KRTAP4-6 ENST00000345847 82.55 85.68 87.34 0.30 0.27 0.28 0.56 0.44 0.31
GPA33 ENST00000367868 82.56 57.66 72.81 0.30 0.56 0.43 0.56 1.48 0.81
SHOX ENST00000381578 82.56 26.15 53.79 0.30 1.19 0.62 0.56 1.08 1.79
UTS2 ENST00000054668 82.57 72.29 80.73 0.30 0.51 0.39 0.56 1.03 0.52
OR8H3 ENST00000313472 82.57 87.82 88.35 0.30 0.24 0.22 0.56 0.37 0.30
KLK7 ENST00000391807 82.58 69.56 79.36 0.30 0.52 0.39 0.56 1.11 0.53
GPR148 ENST00000309926 82.58 90.11 89.47 0.30 0.25 0.18 0.56 0.38 0.24
ZNF716 ENST00000420713 82.59 90.09 89.46 0.30 0.25 0.18 0.56 0.37 0.24
OR3A3 ENST00000291231 82.59 94.35 91.38 0.30 0.23 0.15 0.56 0.24 0.18
C6orf201 ENST00000380175 82.60 75.35 82.36 0.30 0.48 0.33 0.56 0.89 0.44
LYZL4 ENST00000287748 82.60 44.35 64.88 0.30 0.62 0.51 0.56 1.95 1.34
SLC25A34 ENST00000294454 82.61 76.04 82.74 0.30 0.43 0.32 0.56 0.86 0.42
DKKL1 ENST00000221498 82.61 77.60 83.46 0.30 0.42 0.33 0.56 0.79 0.40
OR51B5 ENST00000300773 82.62 95.65 91.91 0.30 0.23 0.14 0.56 0.20 0.17
CCL17 ENST00000219244 82.62 94.86 91.58 0.30 0.23 0.15 0.56 0.24 0.18
CYP2C9 ENST00000260682 82.63 74.74 82.05 0.30 0.54 0.35 0.56 0.96 0.46
OR4M2 ENST00000332663 82.64 96.38 92.17 0.30 0.22 0.14 0.56 0.19 0.16
TNFRSF10C ENST00000356864 82.64 90.10 89.48 0.30 0.25 0.18 0.56 0.38 0.23

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