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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
OR10AG1 ENST00000312345 80.19 94.57 90.45 0.32 0.23 0.14 0.59 0.24 0.21
AMY1C ENST00000370079 80.20 77.30 82.12 0.32 0.42 0.35 0.58 0.77 0.46
CCDC88B ENST00000356786 80.20 24.43 51.44 0.32 1.32 0.63 0.58 1.00 1.91
PLSCR2 ENST00000497985 80.21 68.44 77.56 0.32 0.52 0.37 0.58 1.21 0.57
TSPAN4 ENST00000397404 80.21 73.02 79.93 0.32 0.51 0.37 0.58 1.03 0.52
GEMIN6 ENST00000281950 80.22 87.75 87.15 0.32 0.24 0.28 0.58 0.37 0.30
RARRES2 ENST00000466675 80.22 84.05 85.50 0.32 0.27 0.33 0.58 0.45 0.35
HTR3D ENST00000382489 80.23 69.81 78.28 0.32 0.54 0.38 0.58 1.14 0.55
C15orf54 ENST00000318578 80.23 92.23 89.34 0.32 0.25 0.18 0.58 0.31 0.24
MBD3L1 ENST00000595891 80.24 99.48 92.10 0.32 0.16 0.14 0.58 0.13 0.16
PXDNL ENST00000356297 80.24 58.24 71.79 0.32 0.54 0.46 0.58 1.43 0.81
OR1J2 ENST00000335302 80.25 93.23 89.85 0.32 0.28 0.18 0.58 0.30 0.23
TYW1B ENST00000438904 80.25 87.36 87.00 0.32 0.23 0.28 0.58 0.41 0.30
KRT6B ENST00000252252 80.26 68.94 77.80 0.32 0.54 0.38 0.57 1.16 0.54
IFI27L1 ENST00000555523 80.26 79.97 83.48 0.32 0.37 0.33 0.57 0.61 0.40
DERL3 ENST00000406855 80.27 63.19 74.65 0.32 0.47 0.40 0.57 1.30 0.68
WFDC2 ENST00000372676 80.27 29.50 54.44 0.32 1.09 0.57 0.57 1.39 1.75
RNF113B ENST00000267291 80.28 26.20 52.56 0.32 1.19 0.61 0.57 1.08 1.90
OR6C65 ENST00000379665 80.29 96.22 91.20 0.32 0.22 0.15 0.57 0.20 0.18
ZNF350 ENST00000243644 80.29 45.74 64.29 0.32 0.75 0.51 0.57 2.02 1.35
C9orf116 ENST00000429260 80.30 95.19 90.81 0.33 0.23 0.15 0.57 0.21 0.20
DUOXA2 ENST00000323030 80.30 96.02 91.10 0.33 0.23 0.15 0.58 0.20 0.20
TAF1C ENST00000567759 80.31 71.34 79.15 0.33 0.53 0.38 0.58 1.06 0.54
PPP3R2 ENST00000374806 80.31 93.49 89.99 0.33 0.28 0.18 0.58 0.28 0.22
TULP2 ENST00000221399 80.32 63.70 74.95 0.33 0.49 0.40 0.58 1.24 0.64

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