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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
EPN3 ENST00000268933 68.83 74.63 74.64 0.56 0.54 0.40 0.95 0.98 0.68
HIST1H2AM ENST00000359611 68.83 97.30 86.29 0.56 0.23 0.33 0.95 0.19 0.33
PIGF ENST00000281382 68.84 69.77 71.91 0.57 0.54 0.43 0.95 1.12 0.81
KRT84 ENST00000257951 68.84 64.32 68.57 0.57 0.49 0.47 0.95 1.20 1.05
OR1A2 ENST00000381951 68.85 72.56 73.51 0.57 0.47 0.40 0.95 1.04 0.75
OR10H1 ENST00000334920 68.85 91.27 83.42 0.57 0.23 0.33 0.95 0.34 0.40
SEPT10 ENST00000397712 68.86 66.40 69.86 0.57 0.54 0.46 0.95 1.20 0.92
UBASH3A ENST00000319294 68.87 51.06 60.46 0.57 0.65 0.44 0.95 1.92 1.58
HIGD1B ENST00000253410 68.87 93.87 84.70 0.57 0.25 0.34 0.95 0.26 0.40
AKR1B10 ENST00000359579 68.88 71.44 72.92 0.57 0.53 0.40 0.95 1.06 0.81
GAS2L2 ENST00000254466 68.88 44.02 56.22 0.58 0.61 0.49 0.95 1.97 1.77
CBR3 ENST00000290354 68.89 89.57 82.64 0.57 0.27 0.32 0.95 0.37 0.43
C15orf48 ENST00000344300 68.89 91.51 83.58 0.57 0.23 0.33 0.95 0.32 0.40
AOC2 ENST00000253799 68.90 71.61 73.00 0.57 0.53 0.40 0.95 1.07 0.80
ZDHHC2 ENST00000262096 68.90 38.62 53.19 0.57 0.72 0.61 0.95 1.66 1.88
DDO ENST00000368924 68.91 67.66 70.59 0.57 0.53 0.43 0.95 1.19 0.90
P2RX5 ENST00000225328 68.91 69.25 71.64 0.57 0.57 0.44 0.95 1.14 0.83
PCDHA9 ENST00000532602 68.92 84.94 80.25 0.57 0.27 0.37 0.95 0.44 0.51
TM7SF3 ENST00000343028 68.92 44.96 56.79 0.57 0.68 0.52 0.95 1.97 1.70
C2orf80 ENST00000341287 68.93 83.46 79.47 0.57 0.27 0.38 0.95 0.47 0.52
RNF32 ENST00000405335 68.93 80.82 78.08 0.57 0.35 0.39 0.95 0.57 0.55
NAGPA ENST00000312251 68.94 64.35 68.62 0.57 0.49 0.46 0.95 1.21 1.05
KNG1 ENST00000265023 68.94 49.94 59.75 0.57 0.66 0.49 0.95 2.02 1.66
C2orf40 ENST00000238044 68.95 79.01 77.14 0.57 0.40 0.37 0.95 0.70 0.59
SPATA7 ENST00000393545 68.95 61.96 67.23 0.57 0.56 0.52 0.95 1.36 1.16

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