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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
ZNF850 ENST00000591344 99.56 38.33 71.46 0.12 0.75 0.46 0.13 1.72 0.86
MKI67 ENST00000368654 99.57 39.42 72.13 0.12 0.70 0.43 0.13 1.64 0.81
NLRP11 ENST00000443188 99.57 43.83 74.61 0.12 0.61 0.40 0.13 1.96 0.68
ICAM1 ENST00000264832 99.58 31.74 67.45 0.12 0.95 0.52 0.13 1.48 1.14
APOL3 ENST00000349314 99.58 88.98 97.02 0.12 0.25 0.08 0.13 0.35 0.07
SCGB1D1 ENST00000306238 99.59 97.17 99.65 0.12 0.24 0.12 0.13 0.19 0.04
FBXW12 ENST00000296438 99.59 59.32 82.84 0.12 0.51 0.32 0.13 1.41 0.42
CCL25 ENST00000390669 99.60 69.19 87.53 0.12 0.56 0.28 0.13 1.12 0.30
FLJ27365 ENST00000360737 99.60 69.08 87.49 0.12 0.56 0.28 0.13 1.14 0.30
AL133373.1 ENST00000596306 99.61 97.63 99.75 0.12 0.22 0.12 0.13 0.19 0.04
OR14K1 ENST00000283225 99.61 98.78 99.94 0.12 0.16 0.13 0.13 0.14 0.04
APOC1 ENST00000588750 99.62 81.14 93.14 0.12 0.35 0.14 0.13 0.55 0.15
MICA ENST00000449934 99.62 45.51 75.52 0.12 0.72 0.37 0.13 1.99 0.66
MICB ENST00000252229 99.63 61.20 83.81 0.12 0.53 0.34 0.13 1.41 0.42
PASD1 ENST00000370357 99.63 14.92 57.18 0.12 1.94 0.52 0.13 0.63 1.69
TMEM217 ENST00000336655 99.64 78.81 91.97 0.12 0.42 0.14 0.13 0.71 0.16
ULBP3 ENST00000367339 99.64 90.48 97.63 0.12 0.25 0.09 0.13 0.37 0.06
C3orf30 ENST00000295622 99.65 60.33 83.36 0.12 0.53 0.33 0.13 1.41 0.40
ZNF441 ENST00000357901 99.65 55.81 81.09 0.12 0.52 0.39 0.13 1.58 0.49
RNASE2 ENST00000304625 99.66 98.41 99.92 0.12 0.21 0.12 0.13 0.14 0.04
GIMAP7 ENST00000313543 99.66 97.82 99.73 0.12 0.21 0.12 0.13 0.17 0.04
ICOSLG ENST00000407780 99.67 50.59 78.37 0.12 0.63 0.38 0.13 1.94 0.54
DEC1 ENST00000374016 99.67 94.53 99.05 0.12 0.23 0.11 0.13 0.24 0.04
CD48 ENST00000368046 99.68 74.60 90.20 0.12 0.53 0.18 0.13 0.99 0.21
WFDC10B ENST00000335769 99.68 88.71 96.97 0.12 0.25 0.08 0.13 0.35 0.07

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