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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
ABHD10 ENST00000273359 56.95 64.27 61.28 0.57 0.49 0.44 1.58 1.20 1.48
TXNL4B ENST00000268483 56.95 82.13 72.19 0.57 0.34 0.43 1.58 0.51 0.81
ISLR ENST00000249842 56.96 62.78 60.34 0.57 0.51 0.46 1.58 1.31 1.58
TFPI ENST00000233156 56.97 28.91 41.17 0.57 1.15 0.76 1.58 1.30 2.02
LRRC34 ENST00000446859 56.97 56.22 56.41 0.57 0.52 0.51 1.57 1.56 1.73
RBM23 ENST00000359890 56.98 60.20 58.68 0.57 0.52 0.51 1.57 1.38 1.65
CDHR1 ENST00000372117 56.98 71.63 65.93 0.57 0.53 0.51 1.57 1.07 1.23
OR2A5 ENST00000408906 56.99 85.72 74.21 0.57 0.27 0.39 1.57 0.44 0.69
VCPKMT ENST00000395860 56.99 91.00 77.15 0.57 0.25 0.35 1.57 0.35 0.59
ADAMTS13 ENST00000371929 57.00 35.84 45.08 0.57 0.80 0.70 1.57 1.59 2.02
GUCA1A ENST00000394237 57.00 75.78 68.36 0.57 0.43 0.49 1.57 0.88 1.06
CCR9 ENST00000357632 57.01 64.71 61.57 0.57 0.48 0.46 1.57 1.24 1.48
C3orf70 ENST00000335012 57.01 77.34 69.30 0.57 0.42 0.43 1.57 0.77 0.98
SCNN1A ENST00000360168 57.02 50.42 53.14 0.57 0.65 0.61 1.57 1.95 1.87
TATDN2 ENST00000287652 57.02 43.53 49.19 0.57 0.59 0.72 1.58 1.97 1.84
LONRF2 ENST00000393437 57.03 31.76 42.69 0.57 0.94 0.68 1.58 1.48 2.02
HOXB13 ENST00000290295 57.03 85.35 73.98 0.57 0.25 0.39 1.58 0.45 0.70
SERPINI2 ENST00000476257 57.04 77.79 69.61 0.57 0.42 0.44 1.58 0.79 0.95
ERCC4 ENST00000311895 57.04 49.26 52.44 0.57 0.66 0.61 1.58 2.03 1.92
FAM208B ENST00000328090 57.05 14.38 33.88 0.57 2.05 0.89 1.58 0.61 1.73
CCDC13 ENST00000310232 57.05 38.47 46.41 0.57 0.73 0.67 1.57 1.70 1.90
LMAN2 ENST00000303127 57.06 52.49 54.33 0.57 0.66 0.59 1.57 1.83 1.74
RAD51D ENST00000590016 57.06 63.35 60.80 0.57 0.48 0.43 1.57 1.30 1.60
TTLL11 ENST00000321582 57.07 60.25 58.77 0.57 0.53 0.52 1.57 1.38 1.65
BEX5 ENST00000543160 57.07 96.27 80.00 0.56 0.22 0.35 1.57 0.20 0.52

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