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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
NOC4L ENST00000330579 83.16 27.10 54.72 0.29 1.23 0.57 0.54 1.13 1.73
SOWAHA ENST00000378693 83.17 30.77 56.82 0.29 1.06 0.52 0.54 1.37 1.70
KRTAP10-4 ENST00000400374 83.17 87.12 88.32 0.29 0.22 0.22 0.54 0.41 0.30
DIRAS3 ENST00000370981 83.18 97.69 93.20 0.29 0.21 0.14 0.54 0.19 0.15
ZNF775 ENST00000329630 83.18 35.47 59.66 0.28 0.77 0.49 0.54 1.56 1.67
B3GNT4 ENST00000324189 83.19 79.22 84.55 0.28 0.39 0.34 0.54 0.69 0.39
GNPTG ENST00000204679 83.19 66.11 77.87 0.28 0.54 0.38 0.54 1.20 0.54
AC020907.1 ENST00000313865 83.20 99.59 94.00 0.28 0.16 0.09 0.54 0.12 0.11
HSD3B1 ENST00000369413 83.20 78.62 84.18 0.28 0.40 0.34 0.54 0.74 0.42
TFF3 ENST00000518498 83.21 82.96 86.30 0.28 0.30 0.33 0.54 0.49 0.33
IL17REL ENST00000389983 83.21 38.99 61.84 0.28 0.70 0.47 0.54 1.64 1.46
EFCAB6 ENST00000262726 83.22 63.82 76.61 0.28 0.49 0.37 0.54 1.21 0.61
HGFAC ENST00000382774 83.22 44.85 65.60 0.28 0.68 0.51 0.54 1.98 1.29
C11orf31 ENST00000388857 83.23 88.99 89.21 0.28 0.25 0.19 0.54 0.35 0.25
FFAR3 ENST00000327809 83.23 93.07 91.07 0.28 0.28 0.15 0.54 0.30 0.20
DSPP ENST00000399271 83.24 59.38 74.14 0.28 0.51 0.39 0.54 1.41 0.69
RNASE13 ENST00000382951 83.24 92.17 90.78 0.28 0.25 0.15 0.54 0.31 0.20
OR5T3 ENST00000303059 83.25 88.67 89.06 0.28 0.24 0.19 0.54 0.35 0.26
FOLR3 ENST00000456237 83.25 51.96 69.83 0.28 0.61 0.44 0.54 1.85 0.93
NGRN ENST00000379095 83.26 69.34 79.56 0.28 0.56 0.38 0.54 1.14 0.52
SHROOM2 ENST00000380913 83.27 27.34 54.85 0.28 1.27 0.52 0.54 1.17 1.74
ZNF630 ENST00000409324 83.27 61.38 75.20 0.28 0.54 0.37 0.54 1.40 0.67
CCDC70 ENST00000242819 83.28 88.95 89.22 0.28 0.25 0.19 0.53 0.35 0.25
DHRS4 ENST00000313250 83.28 73.51 81.77 0.28 0.53 0.35 0.53 1.03 0.47
MAP6 ENST00000304771 83.29 30.60 56.77 0.28 1.08 0.52 0.53 1.39 1.70

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