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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
AC137932.1 ENST00000602042 91.43 94.80 96.07 0.15 0.23 0.07 0.20 0.24 0.11
C3orf49 ENST00000295896 91.43 79.05 89.60 0.15 0.40 0.18 0.20 0.70 0.23
C4orf47 ENST00000378850 91.44 57.89 78.10 0.15 0.57 0.39 0.20 1.48 0.55
C17orf105 ENST00000449302 91.44 75.05 86.62 0.15 0.51 0.30 0.20 0.91 0.33
H1FX ENST00000333762 91.45 59.02 77.94 0.15 0.51 0.38 0.20 1.43 0.54
AP000783.1 ENST00000533341 91.45 39.13 67.30 0.15 0.70 0.52 0.20 1.62 1.15
CTD-2054N24.2 ENST00000560059 91.46 96.84 97.11 0.15 0.23 0.08 0.20 0.19 0.07
USP17L5 ENST00000507227 91.46 98.43 97.82 0.15 0.21 0.09 0.20 0.14 0.04
FAM90A26 ENST00000512047 91.47 93.71 95.18 0.15 0.28 0.08 0.20 0.26 0.10
PATE3 ENST00000445202 91.47 86.41 91.93 0.15 0.25 0.14 0.20 0.42 0.17
OVCH1-AS1 ENST00000551108 91.48 50.90 74.27 0.15 0.63 0.39 0.20 1.93 0.69
AL627171.2 ENST00000595378 91.48 98.45 97.84 0.15 0.21 0.09 0.20 0.14 0.04
AC138647.1 ENST00000427937 91.49 95.90 96.69 0.15 0.22 0.08 0.20 0.20 0.08
C20orf78 ENST00000278779 91.49 65.19 81.96 0.15 0.51 0.37 0.20 1.24 0.47
PPP1R3E ENST00000452015 91.50 77.74 88.01 0.15 0.42 0.24 0.20 0.79 0.31
CCDC169 ENST00000503173 91.50 72.01 85.33 0.15 0.51 0.34 0.20 1.04 0.36
NPB ENST00000333383 91.51 93.39 95.44 0.15 0.28 0.08 0.20 0.28 0.11
C2orf74 ENST00000432605 91.51 70.56 84.61 0.15 0.52 0.34 0.20 1.09 0.40
IL11 ENST00000264563 91.52 74.00 86.25 0.15 0.54 0.33 0.20 1.03 0.33
RPP14 ENST00000528153 91.52 78.60 88.41 0.15 0.40 0.22 0.20 0.74 0.30
AC097381.1 ENST00000429019 91.53 98.47 97.60 0.15 0.21 0.09 0.20 0.14 0.06
C9orf62 ENST00000320778 91.53 88.21 92.86 0.15 0.23 0.14 0.20 0.37 0.15
RP11-80A15.1 ENST00000555109 91.54 90.94 94.22 0.15 0.25 0.10 0.20 0.35 0.12
RP11-410N8.4 ENST00000375670 91.54 94.38 96.85 0.15 0.23 0.08 0.21 0.24 0.07
SYCE3 ENST00000406915 91.55 56.77 77.40 0.15 0.53 0.35 0.21 1.55 0.58

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