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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
AC018816.3 ENST00000449914 89.36 91.05 92.94 0.16 0.25 0.14 0.32 0.36 0.15
GPR144 ENST00000334810 89.37 52.54 73.77 0.16 0.66 0.42 0.32 1.82 0.71
CNTNAP3B ENST00000377564 89.37 83.29 89.45 0.16 0.27 0.18 0.32 0.47 0.24
PVRIG ENST00000317271 89.38 62.56 79.27 0.16 0.52 0.38 0.32 1.31 0.54
QRFP ENST00000343079 89.38 98.07 96.66 0.16 0.20 0.08 0.32 0.16 0.08
ZNF20 ENST00000334213 89.39 57.70 76.64 0.16 0.56 0.37 0.32 1.48 0.61
RIMBP3B ENST00000434111 89.39 85.93 90.73 0.16 0.28 0.15 0.32 0.43 0.20
CGB8 ENST00000448456 89.40 95.56 95.22 0.16 0.23 0.08 0.32 0.21 0.10
PRR21 ENST00000408934 89.40 99.51 96.50 0.16 0.16 0.07 0.32 0.13 0.07
CYS1 ENST00000381813 89.41 91.37 93.15 0.16 0.23 0.14 0.32 0.33 0.15
MAGEB16 ENST00000399989 89.41 88.78 91.88 0.16 0.25 0.14 0.32 0.36 0.17
SAGE1 ENST00000535938 89.42 72.74 84.41 0.16 0.48 0.33 0.32 1.04 0.40
FAM227A ENST00000406767 89.42 66.83 81.48 0.16 0.53 0.35 0.32 1.23 0.48
CD22 ENST00000085219 89.43 17.73 52.96 0.16 1.54 0.61 0.32 0.72 1.87
AKAP12 ENST00000402676 89.43 19.69 54.07 0.16 1.43 0.59 0.31 0.74 1.77
TCHH ENST00000368804 89.44 52.53 73.79 0.16 0.66 0.42 0.31 1.83 0.71
DEFB136 ENST00000382209 89.44 93.65 94.32 0.16 0.28 0.10 0.31 0.27 0.12
PLA2G4C ENST00000599111 89.45 52.04 73.55 0.16 0.61 0.40 0.31 1.85 0.74
BOP1 ENST00000307404 89.45 73.72 84.94 0.16 0.52 0.34 0.31 1.03 0.40
C14orf182 ENST00000399206 89.46 90.42 92.69 0.16 0.25 0.14 0.31 0.37 0.15
SPDYE3 ENST00000332397 89.46 59.29 77.62 0.16 0.49 0.38 0.31 1.42 0.56
DEFB108B ENST00000328698 89.47 96.99 95.96 0.16 0.24 0.07 0.30 0.19 0.10
TP53TG3D ENST00000398664 89.47 91.94 93.47 0.16 0.23 0.11 0.30 0.33 0.15
AL445989.1 ENST00000453638 89.48 97.93 96.53 0.16 0.20 0.07 0.30 0.17 0.07
KIAA1875 ENST00000323662 89.48 47.41 70.78 0.16 0.66 0.43 0.30 2.01 0.86

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