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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
CLEC4F ENST00000272367 86.39 71.17 82.16 0.27 0.52 0.35 0.42 1.06 0.45
FSIP2 ENST00000343098 86.40 25.83 55.80 0.27 1.21 0.52 0.42 1.07 1.74
FAM47E ENST00000515604 86.40 47.03 68.73 0.27 0.68 0.46 0.42 1.98 1.05
LPA ENST00000447678 86.41 79.87 86.34 0.27 0.35 0.33 0.42 0.61 0.33
ALG1L ENST00000340333 86.41 96.53 94.22 0.27 0.22 0.10 0.42 0.19 0.12
AKR1C1 ENST00000380872 86.42 81.71 87.23 0.27 0.33 0.28 0.42 0.52 0.31
IGFL1 ENST00000437936 86.42 94.97 93.44 0.27 0.23 0.11 0.42 0.21 0.15
RP11-408E5.4 ENST00000382988 86.43 94.28 93.09 0.27 0.24 0.14 0.42 0.25 0.15
SLC25A29 ENST00000359232 86.43 62.87 77.87 0.27 0.51 0.38 0.42 1.29 0.54
FPR2 ENST00000598776 86.44 86.52 89.60 0.27 0.24 0.18 0.42 0.42 0.23
TEX37 ENST00000303254 86.44 94.60 93.23 0.27 0.23 0.14 0.42 0.24 0.15
OR10H3 ENST00000305892 86.45 96.60 94.27 0.27 0.23 0.10 0.42 0.20 0.12
EXOC3L4 ENST00000380069 86.45 54.91 73.47 0.27 0.57 0.40 0.42 1.63 0.76
FUOM ENST00000368552 86.46 83.95 88.35 0.27 0.28 0.22 0.42 0.46 0.30
PRAM1 ENST00000423345 86.46 37.53 63.06 0.25 0.78 0.51 0.42 1.67 1.39
CEP72 ENST00000264935 86.47 74.92 83.98 0.25 0.53 0.35 0.42 0.94 0.43
RASSF7 ENST00000397583 86.47 79.72 86.31 0.25 0.37 0.33 0.42 0.64 0.33
ICAM2 ENST00000412356 86.48 69.96 81.61 0.25 0.53 0.37 0.42 1.14 0.47
OR4C16 ENST00000314634 86.48 95.35 93.70 0.25 0.24 0.10 0.42 0.21 0.14
INSL6 ENST00000381641 86.49 95.01 93.48 0.25 0.23 0.11 0.42 0.21 0.15
PRSS50 ENST00000460241 86.49 58.99 75.75 0.25 0.52 0.38 0.42 1.43 0.64
TEX26 ENST00000380473 86.50 75.87 84.52 0.25 0.43 0.33 0.42 0.88 0.40
ARSH ENST00000381130 86.50 71.59 82.41 0.25 0.53 0.33 0.41 1.07 0.44
TRIM74 ENST00000285805 86.51 65.23 79.20 0.25 0.51 0.38 0.41 1.24 0.54
C7orf50 ENST00000397098 86.51 83.55 88.18 0.25 0.27 0.23 0.41 0.47 0.30

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