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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
GNG3 ENST00000294117 15.76 69.16 40.64 1.56 0.56 0.81 0.78 1.12 2.05
HSP90AA1 ENST00000334701 15.76 15.62 13.32 1.56 1.87 2.05 0.78 0.68 0.55
SETD7 ENST00000274031 15.77 36.08 23.97 1.56 0.81 1.09 0.78 1.59 1.05
CBFA2T2 ENST00000346541 15.77 9.89 10.41 1.56 2.35 2.18 0.78 0.50 0.43
REST ENST00000309042 15.78 11.02 11.02 1.56 2.10 2.19 0.78 0.52 0.44
RPS2 ENST00000343262 15.78 23.10 17.31 1.56 1.47 1.63 0.78 0.91 0.74
MYH11 ENST00000396324 15.79 12.34 11.68 1.56 2.06 2.23 0.78 0.59 0.47
DENND6A ENST00000311128 15.79 25.46 18.59 1.56 1.25 1.58 0.78 1.06 0.81
GOLPH3 ENST00000265070 15.80 31.11 21.59 1.56 1.01 1.27 0.78 1.36 0.93
GNAI3 ENST00000369851 15.80 33.61 22.86 1.54 0.85 1.19 0.78 1.55 0.97
SLITRK2 ENST00000370490 15.81 30.79 21.43 1.54 1.06 1.33 0.78 1.38 0.91
USP11 ENST00000218348 15.82 2.22 6.34 1.54 3.66 3.09 0.78 0.30 0.32
APBB3 ENST00000354402 15.82 54.86 33.48 1.54 0.57 0.89 0.78 1.63 1.72
HMGN4 ENST00000377575 15.83 91.82 53.25 1.54 0.23 0.61 0.78 0.32 1.88
PLXNA4 ENST00000359827 15.83 7.81 9.27 1.54 2.54 2.32 0.79 0.44 0.38
ANKRD12 ENST00000262126 15.84 5.88 8.22 1.54 2.83 2.58 0.79 0.35 0.37
GPR183 ENST00000376414 15.84 56.91 34.58 1.54 0.56 0.90 0.79 1.53 1.77
EIF4ENIF1 ENST00000397525 15.85 4.74 7.64 1.54 3.28 2.72 0.79 0.32 0.33
RIPK2 ENST00000220751 15.85 21.49 16.50 1.53 1.42 1.71 0.79 0.79 0.69
KCMF1 ENST00000409785 15.86 13.29 12.14 1.53 2.05 2.29 0.79 0.60 0.49
VKORC1L1 ENST00000360768 15.86 24.38 18.05 1.52 1.29 1.70 0.79 1.00 0.78
TADA3 ENST00000301964 15.87 46.76 29.50 1.52 0.72 0.84 0.79 1.97 1.38
GJA1 ENST00000282561 15.87 33.38 22.78 1.52 0.85 1.19 0.79 1.50 0.98
ARL6IP1 ENST00000304414 15.88 46.14 29.16 1.52 0.73 0.84 0.79 2.04 1.32
PRDX6 ENST00000340385 15.88 82.82 48.22 1.52 0.32 0.66 0.79 0.50 1.87

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