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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
NSUN5 ENST00000310326 77.22 69.85 76.63 0.34 0.54 0.37 0.71 1.14 0.61
CCDC109B ENST00000394650 77.23 74.23 79.02 0.34 0.53 0.39 0.71 1.02 0.54
NTN3 ENST00000293973 77.23 61.53 71.97 0.34 0.54 0.42 0.71 1.41 0.81
PTPRJ ENST00000418331 77.24 33.73 55.07 0.34 0.84 0.51 0.71 1.56 1.73
PLA2G5 ENST00000375108 77.24 83.59 83.81 0.34 0.27 0.34 0.71 0.47 0.42
TRAP1 ENST00000246957 77.25 76.76 80.32 0.34 0.40 0.38 0.71 0.83 0.52
PLXNB3 ENST00000538966 77.25 16.96 45.81 0.34 1.66 0.68 0.71 0.73 1.97
FAM149A ENST00000227065 77.26 44.26 61.45 0.34 0.61 0.44 0.71 1.95 1.47
OR51B4 ENST00000380224 77.26 85.02 84.49 0.34 0.25 0.33 0.71 0.45 0.40
ZNF74 ENST00000400451 77.27 47.25 63.42 0.34 0.66 0.49 0.70 2.00 1.37
TNK1 ENST00000576812 77.27 48.76 64.32 0.34 0.63 0.51 0.70 2.01 1.36
EYS ENST00000503581 77.28 44.79 61.76 0.34 0.68 0.46 0.70 1.97 1.47
C11orf88 ENST00000332814 77.28 65.17 74.05 0.34 0.51 0.38 0.70 1.24 0.69
SLC27A3 ENST00000368661 77.29 81.68 82.86 0.34 0.33 0.32 0.69 0.52 0.41
NUDT17 ENST00000334513 77.29 63.23 73.01 0.34 0.47 0.40 0.69 1.31 0.80
C17orf64 ENST00000269127 77.30 90.70 87.17 0.34 0.25 0.28 0.69 0.35 0.31
LBX2 ENST00000460508 77.30 78.74 81.38 0.34 0.42 0.37 0.69 0.73 0.49
LSR ENST00000361790 77.31 46.60 63.02 0.34 0.75 0.51 0.69 2.00 1.39
MLANA ENST00000381477 77.32 96.69 90.10 0.34 0.23 0.18 0.69 0.20 0.22
C9orf152 ENST00000400613 77.32 60.08 71.16 0.34 0.52 0.43 0.69 1.38 0.87
LELP1 ENST00000368747 77.33 85.41 84.71 0.34 0.25 0.34 0.69 0.44 0.40
KRT38 ENST00000246646 77.33 69.57 76.56 0.34 0.52 0.38 0.69 1.10 0.61
TEKT5 ENST00000283025 77.34 85.14 84.58 0.34 0.25 0.34 0.69 0.45 0.40
TMEM218 ENST00000455225 77.34 91.12 87.39 0.34 0.25 0.28 0.69 0.35 0.31
MAD2L1BP ENST00000451025 77.35 75.47 79.72 0.34 0.44 0.38 0.69 0.90 0.53

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