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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
ASB1 ENST00000264607 34.35 61.02 46.37 0.97 0.54 0.67 1.79 1.39 1.90
ZDHHC7 ENST00000564466 34.36 43.54 37.23 0.97 0.61 0.81 1.79 1.97 1.99
TMEM185B ENST00000426077 34.36 10.76 20.69 0.97 2.13 1.47 1.79 0.51 0.87
ARFGAP2 ENST00000524782 34.37 27.51 29.09 0.97 1.25 0.84 1.80 1.17 1.32
ACSBG1 ENST00000258873 34.37 31.55 31.16 0.97 0.95 0.85 1.80 1.43 1.54
RHOBTB1 ENST00000337910 34.38 31.94 31.38 0.99 0.94 0.87 1.80 1.48 1.56
PPP1R3C ENST00000238994 34.38 52.51 41.65 0.99 0.66 0.72 1.80 1.83 2.01
HLA-E ENST00000376630 34.39 31.76 31.30 0.99 0.95 0.87 1.79 1.47 1.55
POLA1 ENST00000379059 34.39 0.13 15.07 0.99 4.10 1.87 1.80 0.28 0.62
RANBP10 ENST00000317506 34.40 14.07 22.43 0.99 2.07 1.15 1.80 0.59 0.97
TANC1 ENST00000263635 34.40 18.60 24.57 0.99 1.48 1.06 1.80 0.76 1.10
RBM41 ENST00000372479 34.41 13.58 22.11 0.99 2.05 1.15 1.80 0.59 0.96
XBP1 ENST00000216037 34.41 41.40 36.02 0.99 0.62 0.87 1.80 1.80 1.79
AVL9 ENST00000318709 34.42 28.48 29.62 0.99 1.16 0.85 1.80 1.24 1.39
INO80B ENST00000233331 34.42 22.60 26.67 0.99 1.47 0.99 1.80 0.86 1.26
NKX2-2 ENST00000377142 34.43 26.38 28.56 1.00 1.18 0.80 1.80 1.09 1.34
DPM3 ENST00000368399 34.44 76.30 54.95 1.00 0.43 0.51 1.80 0.86 1.74
GPN3 ENST00000543199 34.44 56.90 44.09 1.00 0.56 0.61 1.80 1.54 2.03
KIAA0247 ENST00000342745 34.45 26.28 28.53 1.00 1.19 0.78 1.80 1.08 1.32
BPGM ENST00000393132 34.45 53.88 42.42 0.99 0.65 0.68 1.80 1.70 2.01
AASS ENST00000393376 34.46 43.02 36.95 0.97 0.61 0.80 1.80 1.89 1.95
GJA4 ENST00000342280 34.46 44.51 37.72 0.99 0.63 0.84 1.80 1.98 2.01
KIAA1324 ENST00000369939 34.47 37.92 34.44 0.99 0.80 0.90 1.80 1.70 1.75
DLAT ENST00000280346 34.47 45.77 38.42 0.99 0.75 0.84 1.80 2.02 2.04
MLH3 ENST00000355774 34.48 29.44 30.14 0.99 1.09 0.81 1.80 1.38 1.46

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