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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
FBXO2 ENST00000354287 64.70 50.39 57.48 0.54 0.66 0.51 1.18 1.95 1.65
WDR73 ENST00000434634 64.70 69.94 69.49 0.54 0.53 0.44 1.18 1.14 0.98
ARHGAP4 ENST00000370028 64.71 13.90 37.57 0.54 2.05 0.84 1.18 0.60 2.01
FXYD1 ENST00000588081 64.71 44.02 53.79 0.54 0.61 0.62 1.18 1.97 1.79
IL27 ENST00000356897 64.72 24.61 43.04 0.54 1.30 0.66 1.17 1.05 2.02
RRP8 ENST00000254605 64.72 70.78 69.99 0.54 0.48 0.47 1.17 1.08 0.92
MIEN1 ENST00000394231 64.73 38.27 50.51 0.54 0.75 0.67 1.17 1.70 1.86
URGCP-MRPS24 ENST00000603700 64.73 72.25 70.84 0.54 0.51 0.43 1.17 1.04 0.86
SAG ENST00000409110 64.74 75.03 72.54 0.54 0.52 0.46 1.17 0.92 0.83
OR13C9 ENST00000259362 64.74 79.42 75.01 0.54 0.38 0.39 1.17 0.67 0.66
ATP5EP2 ENST00000381026 64.75 88.74 80.07 0.54 0.25 0.35 1.17 0.35 0.52
TUBB1 ENST00000217133 64.75 74.24 72.13 0.54 0.53 0.43 1.17 1.02 0.81
PCDHGA3 ENST00000253812 64.76 48.56 56.46 0.54 0.65 0.52 1.17 2.01 1.70
MNS1 ENST00000260453 64.76 72.21 70.82 0.54 0.52 0.43 1.17 1.04 0.87
FAM64A ENST00000250056 64.77 58.97 62.84 0.54 0.52 0.49 1.17 1.42 1.40
ACN9 ENST00000432641 64.77 91.56 81.52 0.54 0.23 0.35 1.17 0.32 0.48
GSTK1 ENST00000479303 64.78 74.69 72.43 0.54 0.54 0.44 1.18 0.96 0.83
ZDHHC12 ENST00000372663 64.78 54.86 60.30 0.54 0.57 0.47 1.18 1.62 1.59
ANKRD37 ENST00000335174 64.79 71.62 70.51 0.54 0.53 0.43 1.18 1.07 0.91
DLGAP2 ENST00000421627 64.80 5.81 33.42 0.54 2.86 0.87 1.18 0.35 1.70
HLA-DOB ENST00000438763 64.80 73.72 71.84 0.54 0.52 0.44 1.18 1.03 0.82
PARVG ENST00000444313 64.81 47.88 56.04 0.54 0.59 0.49 1.19 1.97 1.76
DACH2 ENST00000373125 64.81 32.13 47.23 0.54 0.89 0.67 1.19 1.46 1.88
CWH43 ENST00000226432 64.82 67.72 68.28 0.54 0.52 0.52 1.19 1.19 1.07
FOXS1 ENST00000375978 64.82 55.65 60.83 0.56 0.53 0.43 1.19 1.60 1.61

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