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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
ACAP3 ENST00000354700 70.38 26.02 46.94 0.49 1.20 0.70 0.91 1.10 1.87
WNT10A ENST00000258411 70.38 74.37 75.29 0.49 0.53 0.37 0.91 1.00 0.66
SH2D1B ENST00000367929 70.39 63.91 69.28 0.49 0.48 0.43 0.91 1.22 0.98
SLC25A2 ENST00000239451 70.39 71.02 73.50 0.49 0.49 0.40 0.91 1.07 0.75
VAMP3 ENST00000054666 70.40 72.96 74.60 0.49 0.51 0.40 0.91 1.03 0.68
SLC2A8 ENST00000373371 70.40 60.34 67.11 0.49 0.53 0.51 0.91 1.41 1.17
CEP89 ENST00000305768 70.41 66.71 70.92 0.49 0.56 0.43 0.91 1.21 0.86
ELOVL3 ENST00000370005 70.41 55.33 64.14 0.49 0.57 0.52 0.91 1.61 1.37
TMEM130 ENST00000416379 70.42 66.34 70.73 0.49 0.54 0.43 0.91 1.20 0.86
GEN1 ENST00000381254 70.43 51.56 61.72 0.49 0.62 0.46 0.91 1.87 1.46
HLA-DRB5 ENST00000374975 70.43 89.76 83.45 0.49 0.27 0.33 0.91 0.37 0.40
TKTL1 ENST00000369915 70.44 2.64 34.75 0.49 3.55 0.90 0.91 0.29 1.76
EIF3CL ENST00000398943 70.44 86.63 81.92 0.49 0.24 0.37 0.91 0.40 0.46
TP53TG5 ENST00000372726 70.45 72.07 74.11 0.49 0.52 0.39 0.91 1.03 0.69
ABHD1 ENST00000316470 70.45 95.07 86.01 0.49 0.23 0.33 0.91 0.21 0.33
TMEM128 ENST00000254742 70.46 83.19 80.16 0.49 0.28 0.35 0.91 0.47 0.53
UCN ENST00000296099 70.46 81.86 79.42 0.49 0.35 0.39 0.91 0.51 0.52
RCAN2 ENST00000371374 70.47 22.52 45.14 0.49 1.48 0.70 0.91 0.84 2.00
LSMEM1 ENST00000312849 70.47 90.25 83.75 0.49 0.25 0.34 0.91 0.38 0.41
DFNA5 ENST00000342947 70.48 61.06 67.64 0.49 0.54 0.51 0.91 1.39 1.13
SLC22A18 ENST00000380574 70.48 65.29 70.10 0.49 0.51 0.46 0.91 1.24 0.90
LIN7B ENST00000221459 70.49 21.34 44.40 0.49 1.43 0.59 0.91 0.80 2.04
CCDC63 ENST00000308208 70.49 69.83 72.92 0.49 0.54 0.40 0.91 1.14 0.81
ZNF662 ENST00000328199 70.50 75.61 76.07 0.49 0.44 0.38 0.91 0.91 0.62
KLK6 ENST00000376851 70.50 55.62 64.34 0.49 0.53 0.51 0.91 1.60 1.35

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