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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
SERPINE3 ENST00000521255 64.05 57.18 61.33 0.57 0.56 0.44 1.19 1.49 1.48
STRC ENST00000450892 64.06 48.38 55.89 0.57 0.63 0.49 1.19 2.00 1.75
C2orf43 ENST00000237822 64.06 49.29 56.51 0.57 0.65 0.52 1.19 2.02 1.70
GUCA1B ENST00000230361 64.07 68.13 68.06 0.57 0.53 0.51 1.19 1.21 1.10
HHIPL2 ENST00000343410 64.07 78.56 74.17 0.57 0.40 0.39 1.19 0.73 0.69
GPR89B ENST00000314163 64.08 70.09 69.18 0.57 0.53 0.44 1.19 1.13 0.99
HDGFRP2 ENST00000301284 64.08 18.37 39.58 0.57 1.48 0.80 1.20 0.75 2.04
ARSK ENST00000380009 64.09 60.12 63.19 0.57 0.52 0.49 1.20 1.39 1.36
KLK13 ENST00000595793 64.09 62.47 64.62 0.57 0.53 0.51 1.20 1.31 1.32
ZNF408 ENST00000311764 64.10 43.11 53.00 0.57 0.61 0.61 1.20 1.90 1.87
THAP5 ENST00000415914 64.10 62.64 64.73 0.57 0.51 0.49 1.20 1.31 1.32
IL20 ENST00000367098 64.11 84.12 77.27 0.57 0.27 0.35 1.20 0.45 0.58
ADAMTS16 ENST00000274181 64.11 20.75 40.62 0.57 1.46 0.81 1.20 0.81 2.05
GTF2H2C ENST00000510979 64.12 59.10 62.47 0.57 0.49 0.48 1.20 1.43 1.40
SLC46A2 ENST00000374228 64.12 84.70 77.63 0.57 0.27 0.38 1.20 0.42 0.55
ZCWPW2 ENST00000383768 64.13 57.16 61.31 0.57 0.56 0.44 1.20 1.51 1.48
TGM7 ENST00000452443 64.13 63.53 65.32 0.57 0.49 0.53 1.20 1.25 1.32
C20orf196 ENST00000303142 64.14 55.94 60.55 0.57 0.49 0.44 1.20 1.56 1.58
B9D1 ENST00000261499 64.14 51.99 58.12 0.57 0.61 0.48 1.20 1.86 1.65
BARD1 ENST00000260947 64.15 73.26 71.17 0.57 0.54 0.44 1.20 1.02 0.86
HINT3 ENST00000229633 64.15 88.74 79.76 0.57 0.25 0.38 1.20 0.35 0.53
FIGNL1 ENST00000419119 64.16 42.69 52.76 0.57 0.61 0.61 1.20 1.92 1.89
CCDC36 ENST00000438782 64.17 34.41 48.15 0.57 0.84 0.66 1.20 1.56 1.87
BCL2A1 ENST00000267953 64.17 50.15 57.06 0.57 0.67 0.51 1.20 1.99 1.71
TMEM30B ENST00000555868 64.18 76.14 72.91 0.57 0.43 0.40 1.19 0.87 0.81

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