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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
FAM211B ENST00000318753 81.35 97.05 91.95 0.33 0.24 0.14 0.60 0.19 0.16
IGFBP1 ENST00000275525 81.36 68.53 78.21 0.33 0.53 0.38 0.60 1.19 0.55
TRIM40 ENST00000307859 81.36 90.20 88.92 0.33 0.25 0.19 0.60 0.38 0.28
ZNF334 ENST00000347606 81.37 59.17 73.01 0.33 0.49 0.40 0.60 1.44 0.80
LCE4A ENST00000368777 81.37 98.80 93.26 0.33 0.16 0.14 0.60 0.14 0.15
OR10G7 ENST00000330487 81.38 91.89 89.73 0.33 0.23 0.18 0.60 0.32 0.23
CDX4 ENST00000373514 81.39 77.96 83.04 0.33 0.42 0.30 0.60 0.79 0.40
DACT3 ENST00000391916 81.39 34.02 57.67 0.33 0.82 0.51 0.60 1.55 1.66
CTSB ENST00000353047 81.40 75.05 81.62 0.33 0.51 0.37 0.60 0.92 0.47
SPINK4 ENST00000379721 81.40 64.95 76.26 0.33 0.49 0.37 0.60 1.24 0.61
OR6C2 ENST00000322678 81.41 74.57 81.35 0.33 0.52 0.38 0.60 1.00 0.49
CYP11B2 ENST00000323110 81.41 81.28 84.68 0.33 0.33 0.34 0.60 0.54 0.40
IGSF6 ENST00000268389 81.42 58.78 72.83 0.33 0.54 0.43 0.60 1.42 0.80
KRTAP23-1 ENST00000334160 81.42 97.85 92.36 0.33 0.21 0.14 0.60 0.17 0.15
NUDT7 ENST00000268533 81.43 92.71 90.12 0.33 0.29 0.18 0.60 0.30 0.22
ANO7 ENST00000274979 81.43 73.29 80.68 0.33 0.56 0.39 0.60 1.02 0.52
ALLC ENST00000252505 81.44 78.03 83.11 0.33 0.42 0.30 0.60 0.77 0.40
TOMM5 ENST00000544379 81.44 76.02 82.11 0.33 0.43 0.35 0.60 0.86 0.46
REG1A ENST00000233735 81.45 82.27 85.20 0.33 0.34 0.34 0.60 0.52 0.37
PRSS1 ENST00000311737 81.45 93.71 90.65 0.33 0.28 0.15 0.60 0.26 0.20
ELSPBP1 ENST00000339841 81.46 83.70 85.87 0.33 0.27 0.33 0.60 0.47 0.33
HSD17B6 ENST00000554643 81.46 36.37 59.09 0.33 0.82 0.49 0.60 1.63 1.68
HHLA2 ENST00000357759 81.47 56.18 71.29 0.33 0.52 0.43 0.60 1.56 0.87
SHC2 ENST00000264554 81.47 68.24 78.05 0.33 0.52 0.39 0.60 1.21 0.54
MEFV ENST00000219596 81.48 62.50 74.91 0.33 0.53 0.39 0.60 1.31 0.64

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