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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
GBP2 ENST00000370466 87.81 54.70 74.08 0.23 0.58 0.38 0.37 1.65 0.69
OR2T2 ENST00000342927 87.82 83.68 88.88 0.23 0.27 0.19 0.37 0.47 0.28
ENO4 ENST00000409522 87.82 78.77 86.49 0.23 0.42 0.30 0.37 0.71 0.33
AP000695.1 ENST00000595927 87.83 99.74 96.60 0.23 0.17 0.08 0.36 0.11 0.08
GAMT ENST00000447102 87.83 68.88 81.75 0.23 0.54 0.35 0.36 1.17 0.47
TNP2 ENST00000312693 87.84 89.96 91.73 0.23 0.25 0.14 0.36 0.37 0.18
DTHD1 ENST00000456874 87.84 44.78 68.29 0.23 0.67 0.52 0.36 1.97 1.07
OR5M10 ENST00000526812 87.85 96.66 95.00 0.23 0.23 0.09 0.36 0.20 0.10
PGBD4 ENST00000397766 87.85 90.69 92.01 0.23 0.25 0.14 0.36 0.36 0.16
IFNB1 ENST00000380232 87.86 99.38 96.44 0.23 0.16 0.07 0.36 0.12 0.09
FAM200A ENST00000449309 87.86 68.71 81.66 0.23 0.53 0.37 0.36 1.17 0.47
CD300E ENST00000328630 87.87 54.23 73.83 0.23 0.62 0.42 0.36 1.70 0.71
KRTAP9-3 ENST00000411528 87.87 97.62 95.53 0.23 0.22 0.08 0.36 0.20 0.11
MROH2A ENST00000389758 87.88 39.15 64.95 0.23 0.70 0.51 0.36 1.62 1.32
PLCXD1 ENST00000381657 87.88 83.03 88.57 0.23 0.32 0.22 0.36 0.49 0.28
MAGEB5 ENST00000602297 87.89 98.51 95.66 0.23 0.21 0.07 0.36 0.15 0.11
SPRR2B ENST00000341611 87.89 98.57 95.92 0.23 0.20 0.07 0.36 0.15 0.10
KRTAP22-1 ENST00000334680 87.90 97.83 95.68 0.23 0.21 0.07 0.36 0.17 0.11
TBC1D29 ENST00000580161 87.90 81.72 87.95 0.23 0.33 0.24 0.36 0.52 0.32
HES4 ENST00000428771 87.91 96.90 95.14 0.23 0.23 0.09 0.35 0.19 0.10
ZNF107 ENST00000395391 87.91 94.06 93.79 0.23 0.25 0.10 0.35 0.26 0.13
CYP4F2 ENST00000221700 87.92 74.36 84.49 0.23 0.53 0.33 0.35 1.00 0.40
CTRB1 ENST00000361017 87.92 92.50 92.97 0.23 0.28 0.14 0.35 0.30 0.15
KRTAP4-8 ENST00000333822 87.93 75.40 85.04 0.23 0.46 0.33 0.35 0.90 0.39
CD5 ENST00000347785 87.93 56.96 75.38 0.22 0.56 0.37 0.35 1.53 0.66

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