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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
OR8B3 ENST00000354597 78.13 84.13 84.48 0.34 0.27 0.33 0.66 0.45 0.40
IGFBPL1 ENST00000377694 78.13 84.59 84.71 0.34 0.28 0.34 0.66 0.42 0.40
ENTPD2 ENST00000355097 78.14 79.75 82.31 0.34 0.37 0.33 0.66 0.64 0.44
CYP2E1 ENST00000463117 78.14 57.24 69.93 0.34 0.56 0.46 0.66 1.49 0.92
OVGP1 ENST00000369732 78.15 38.55 58.38 0.34 0.73 0.51 0.66 1.66 1.65
CBWD2 ENST00000259199 78.15 45.55 62.83 0.34 0.72 0.48 0.66 1.99 1.40
PDGFRL ENST00000541323 78.16 91.07 87.77 0.34 0.25 0.24 0.66 0.36 0.32
CARS2 ENST00000257347 78.16 45.70 62.96 0.34 0.75 0.51 0.66 2.02 1.39
GZMA ENST00000274306 78.17 85.73 85.31 0.34 0.27 0.34 0.66 0.44 0.36
DVL1 ENST00000378891 78.17 36.66 57.31 0.34 0.77 0.51 0.66 1.66 1.68
UCMA ENST00000378681 78.18 82.70 83.83 0.34 0.34 0.34 0.66 0.50 0.42
YY2 ENST00000429584 78.18 49.00 65.03 0.34 0.66 0.51 0.66 2.04 1.31
ACRV1 ENST00000533904 78.19 75.79 80.31 0.34 0.43 0.38 0.66 0.88 0.52
FBXL6 ENST00000331890 78.19 61.15 72.36 0.34 0.53 0.44 0.66 1.40 0.83
FAIM3 ENST00000367091 78.20 56.13 69.29 0.34 0.52 0.43 0.67 1.55 0.98
SLC34A3 ENST00000538474 78.20 75.35 80.11 0.34 0.48 0.35 0.67 0.89 0.52
ARHGEF5 ENST00000056217 78.21 51.66 66.62 0.34 0.62 0.52 0.67 1.88 1.20
OR10G9 ENST00000375024 78.21 94.34 89.38 0.34 0.24 0.18 0.67 0.24 0.24
C3AR1 ENST00000307637 78.22 82.38 83.71 0.34 0.34 0.34 0.67 0.52 0.40
ACOT4 ENST00000326303 78.22 84.72 84.85 0.34 0.27 0.34 0.67 0.42 0.40
ATP5J2 ENST00000292475 78.23 80.35 82.71 0.34 0.37 0.32 0.67 0.59 0.42
NXPE1 ENST00000251921 78.23 91.51 88.03 0.34 0.23 0.24 0.67 0.32 0.31
RTDR1 ENST00000216036 78.24 60.90 72.25 0.34 0.56 0.43 0.67 1.41 0.82
OR6C6 ENST00000358433 78.24 77.38 81.16 0.35 0.42 0.39 0.67 0.76 0.49
SCIN ENST00000297029 78.25 83.40 84.07 0.35 0.27 0.35 0.67 0.47 0.42

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