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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
NOP16 ENST00000510123 62.76 64.98 65.42 0.59 0.49 0.53 1.28 1.24 1.32
AOAH ENST00000258749 62.77 52.66 57.71 0.59 0.68 0.49 1.28 1.80 1.68
GABRE ENST00000370328 62.77 57.14 60.43 0.59 0.56 0.44 1.28 1.50 1.58
BHMT ENST00000274353 62.78 74.95 71.35 0.59 0.53 0.43 1.29 0.93 0.87
KRTAP11-1 ENST00000332378 62.78 81.46 75.05 0.59 0.33 0.39 1.29 0.55 0.66
SLA2 ENST00000262866 62.79 38.90 49.79 0.59 0.70 0.65 1.29 1.65 1.88
OR1L6 ENST00000304720 62.79 94.74 82.14 0.59 0.23 0.35 1.29 0.24 0.45
RHBG ENST00000368249 62.80 83.45 76.16 0.59 0.27 0.37 1.30 0.47 0.62
METTL7B ENST00000394252 62.80 55.67 59.52 0.59 0.52 0.49 1.30 1.60 1.70
HBA1 ENST00000320868 62.81 92.18 80.80 0.59 0.25 0.39 1.30 0.31 0.52
FASTKD1 ENST00000453153 62.81 72.51 69.89 0.59 0.47 0.46 1.30 1.03 0.92
LRRC6 ENST00000250173 62.82 57.39 60.65 0.59 0.54 0.44 1.29 1.49 1.61
SLC5A5 ENST00000222248 62.82 29.05 44.44 0.59 1.14 0.61 1.29 1.31 2.04
CAPN11 ENST00000398776 62.83 62.80 64.09 0.59 0.51 0.52 1.29 1.31 1.37
OR4D11 ENST00000313253 62.83 95.57 82.59 0.59 0.23 0.32 1.29 0.21 0.43
ADAT1 ENST00000307921 62.84 65.69 65.89 0.59 0.53 0.51 1.29 1.23 1.24
TNP1 ENST00000236979 62.84 88.37 78.85 0.59 0.23 0.39 1.29 0.37 0.52
PTMA ENST00000341369 62.85 67.10 66.69 0.59 0.54 0.54 1.29 1.23 1.20
FTL ENST00000331825 62.85 96.59 83.08 0.59 0.23 0.30 1.29 0.19 0.40
ESYT3 ENST00000389567 62.86 60.96 62.89 0.59 0.54 0.51 1.29 1.41 1.40
MC2R ENST00000327606 62.86 91.22 80.35 0.59 0.23 0.38 1.29 0.34 0.52
METTL15 ENST00000407364 62.87 73.25 70.35 0.59 0.54 0.43 1.29 1.02 0.91
ARHGAP9 ENST00000393791 62.87 46.69 54.31 0.59 0.73 0.59 1.29 1.97 1.73
TOMM20L ENST00000360945 62.88 82.53 75.70 0.59 0.34 0.38 1.29 0.52 0.64
CCDC62 ENST00000253079 62.88 59.03 61.69 0.59 0.51 0.46 1.28 1.43 1.46

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