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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
AC016757.3 ENST00000409070 93.51 96.61 95.91 0.13 0.23 0.07 0.14 0.20 0.10
RP11-10A14.4 ENST00000518496 92.22 93.73 95.92 0.15 0.28 0.07 0.18 0.26 0.10
SPRR2B ENST00000341611 87.89 98.57 95.92 0.23 0.20 0.07 0.36 0.15 0.10
RP11-817J15.3 ENST00000537079 92.52 95.15 95.93 0.15 0.23 0.07 0.18 0.21 0.10
ADM5 ENST00000420022 97.87 88.53 95.94 0.11 0.23 0.07 0.11 0.36 0.10
OR4C46 ENST00000328188 88.94 97.46 95.94 0.19 0.22 0.07 0.32 0.19 0.10
GJD3 ENST00000578689 93.98 94.40 95.95 0.10 0.23 0.07 0.13 0.24 0.10
APOL1 ENST00000319136 99.22 87.21 95.95 0.11 0.20 0.07 0.12 0.41 0.10
ZBED3 ENST00000255198 92.60 94.96 95.96 0.15 0.23 0.07 0.18 0.21 0.10
DEFB108B ENST00000328698 89.47 96.99 95.96 0.16 0.24 0.07 0.30 0.19 0.10
ZNF121 ENST00000320451 99.49 86.99 95.97 0.11 0.22 0.07 0.13 0.40 0.10
MAGEC3 ENST00000298296 97.96 88.51 95.97 0.11 0.23 0.07 0.11 0.36 0.10
C16orf91 ENST00000310355 97.14 89.35 95.98 0.10 0.27 0.07 0.11 0.37 0.10
RP11-536G4.1 ENST00000553095 91.19 94.32 95.98 0.15 0.24 0.07 0.21 0.25 0.10
AL592284.1 ENST00000538264 92.15 93.91 95.99 0.15 0.25 0.07 0.19 0.26 0.10
ZNF547 ENST00000282282 94.92 91.59 95.99 0.10 0.23 0.07 0.12 0.33 0.11
CLLU1OS ENST00000378487 94.95 91.59 96.00 0.10 0.23 0.07 0.12 0.32 0.11
hsa-mir-150 ENST00000602157 90.18 96.49 96.00 0.16 0.22 0.07 0.25 0.19 0.11
FAM27B ENST00000377484 92.45 96.41 96.01 0.15 0.22 0.07 0.18 0.19 0.11
MS4A14 ENST00000531783 98.76 87.83 96.01 0.10 0.24 0.07 0.11 0.38 0.11
PP13004 ENST00000381493 93.39 92.97 96.02 0.13 0.29 0.07 0.15 0.30 0.11
CGB2 ENST00000359342 94.35 92.24 96.02 0.10 0.25 0.07 0.11 0.31 0.11
CSN1S1 ENST00000246891 98.64 87.96 96.03 0.10 0.25 0.07 0.11 0.37 0.11
PGA4 ENST00000378149 89.75 92.97 96.03 0.16 0.29 0.07 0.28 0.30 0.11
CCL13 ENST00000225844 96.39 90.21 96.04 0.10 0.25 0.07 0.11 0.38 0.11

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