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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
HP ENST00000355906 73.22 53.93 65.01 0.34 0.65 0.51 0.79 1.70 1.31
TMEM14B ENST00000379542 73.22 96.43 87.97 0.34 0.22 0.24 0.79 0.19 0.32
RAMP2 ENST00000253796 73.23 61.05 69.25 0.34 0.54 0.44 0.79 1.39 0.97
SLC26A11 ENST00000361193 73.23 76.39 77.99 0.34 0.43 0.38 0.79 0.86 0.54
SLC27A6 ENST00000262462 73.24 71.80 75.46 0.34 0.51 0.38 0.79 1.07 0.66
ZNF605 ENST00000392321 73.25 55.51 66.01 0.34 0.57 0.51 0.79 1.60 1.22
B3GNT3 ENST00000318683 73.25 29.14 50.22 0.34 1.13 0.65 0.79 1.34 1.90
DDX51 ENST00000397333 73.26 53.50 64.77 0.34 0.65 0.49 0.79 1.71 1.32
OR10X1 ENST00000368150 73.26 92.08 85.94 0.34 0.24 0.33 0.79 0.32 0.33
EPHX3 ENST00000221730 73.27 84.88 82.46 0.34 0.27 0.33 0.79 0.44 0.44
ZNF79 ENST00000342483 73.27 35.30 53.70 0.34 0.76 0.62 0.79 1.58 1.82
TTLL10 ENST00000379290 73.28 62.79 70.33 0.34 0.51 0.43 0.79 1.31 0.90
FTSJ2 ENST00000242257 73.28 87.02 83.52 0.34 0.22 0.33 0.79 0.40 0.40
TPRKB ENST00000272424 73.29 74.42 76.97 0.34 0.53 0.37 0.79 1.00 0.61
FUT7 ENST00000314412 73.29 62.69 70.22 0.34 0.51 0.43 0.79 1.31 0.91
PCDHB5 ENST00000231134 73.30 65.41 71.94 0.34 0.53 0.43 0.79 1.25 0.81
RNF151 ENST00000569714 73.30 83.65 81.84 0.34 0.27 0.37 0.79 0.47 0.47
TMEM160 ENST00000253047 73.31 70.37 74.74 0.34 0.52 0.40 0.80 1.09 0.66
OR51D1 ENST00000357605 73.31 81.44 80.68 0.34 0.33 0.39 0.80 0.54 0.52
PIGB ENST00000164305 73.32 60.32 68.83 0.34 0.53 0.46 0.80 1.39 1.05
RNF207 ENST00000377939 73.32 50.18 62.67 0.34 0.67 0.51 0.80 1.99 1.39
MLN ENST00000430124 73.33 81.07 80.52 0.34 0.35 0.39 0.80 0.55 0.51
SIRT5 ENST00000606117 73.33 64.78 71.59 0.34 0.49 0.44 0.80 1.24 0.83
TIGIT ENST00000486257 73.34 58.63 67.88 0.34 0.54 0.51 0.80 1.42 1.11
ARID3C ENST00000378909 73.34 72.06 75.69 0.34 0.52 0.38 0.80 1.03 0.64

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