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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
OR5AS1 ENST00000313555 83.29 90.04 89.76 0.28 0.25 0.18 0.53 0.37 0.23
HCRT ENST00000293330 83.30 91.50 90.46 0.28 0.23 0.14 0.53 0.32 0.21
PRSS54 ENST00000219301 83.30 53.65 70.80 0.28 0.63 0.43 0.53 1.70 0.86
OR4C11 ENST00000302231 83.31 94.22 91.61 0.28 0.25 0.14 0.53 0.25 0.18
FAM71C ENST00000324341 83.31 54.33 71.29 0.28 0.62 0.43 0.52 1.68 0.87
ZNF169 ENST00000395395 83.32 73.96 82.01 0.28 0.53 0.37 0.52 1.02 0.47
CTSW ENST00000307886 83.32 77.98 83.93 0.28 0.42 0.35 0.52 0.78 0.43
ATP5L2 ENST00000505920 83.33 97.05 92.93 0.28 0.24 0.14 0.52 0.19 0.15
IFNL1 ENST00000333625 83.33 79.69 84.87 0.28 0.37 0.34 0.52 0.65 0.40
CYP11B1 ENST00000292427 83.34 52.95 70.47 0.28 0.63 0.43 0.52 1.78 0.91
COMTD1 ENST00000372538 83.34 74.58 82.34 0.28 0.53 0.33 0.52 1.00 0.44
ARRDC5 ENST00000381781 83.35 78.65 84.31 0.28 0.40 0.33 0.52 0.74 0.41
ABHD16B ENST00000369916 83.35 65.25 77.53 0.28 0.51 0.35 0.52 1.24 0.57
C16orf13 ENST00000397666 83.36 86.84 88.26 0.28 0.23 0.23 0.52 0.40 0.30
TEKT4 ENST00000295201 83.36 80.86 85.48 0.28 0.35 0.33 0.52 0.57 0.35
LMF2 ENST00000474879 83.37 95.34 92.06 0.29 0.24 0.14 0.52 0.21 0.16
KIAA1107 ENST00000370378 83.37 18.87 50.14 0.29 1.53 0.62 0.52 0.76 1.90
C5AR2 ENST00000595464 83.38 76.86 83.47 0.29 0.43 0.33 0.52 0.81 0.40
ACTRT1 ENST00000371124 83.38 82.45 86.15 0.30 0.34 0.33 0.52 0.52 0.33
CCDC37 ENST00000352312 83.39 60.26 74.73 0.30 0.53 0.40 0.52 1.38 0.67
PCDHB12 ENST00000239450 83.39 73.67 81.91 0.30 0.52 0.37 0.51 1.03 0.46
CXCL5 ENST00000296027 83.40 95.14 92.01 0.30 0.23 0.14 0.51 0.21 0.16
HIST1H2AA ENST00000297012 83.40 97.07 92.98 0.30 0.24 0.14 0.51 0.19 0.15
PPP5D1 ENST00000414155 83.41 69.32 79.63 0.30 0.56 0.38 0.51 1.14 0.53
DNLZ ENST00000371738 83.42 92.76 91.03 0.30 0.29 0.15 0.51 0.30 0.20

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