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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
CD27 ENST00000266557 79.16 52.89 67.95 0.33 0.65 0.51 0.61 1.80 1.10
LGALS7B ENST00000314980 79.16 84.18 85.03 0.33 0.27 0.33 0.61 0.44 0.39
PRRG2 ENST00000246794 79.17 78.51 82.22 0.33 0.42 0.35 0.61 0.74 0.44
OTOR ENST00000246081 79.17 82.11 83.92 0.33 0.34 0.35 0.61 0.50 0.43
SLC2A4RG ENST00000266077 79.18 28.36 53.20 0.33 1.16 0.61 0.61 1.22 1.89
RAB26 ENST00000210187 79.18 86.47 86.06 0.33 0.24 0.33 0.61 0.42 0.33
SLC22A16 ENST00000368919 79.19 90.75 88.11 0.33 0.25 0.23 0.61 0.35 0.30
MAGEL2 ENST00000532292 79.20 12.92 44.63 0.33 2.07 0.62 0.61 0.59 2.06
PIK3IP1 ENST00000215912 79.20 49.03 65.74 0.33 0.66 0.51 0.61 2.03 1.26
ACSF3 ENST00000317447 79.21 89.62 87.55 0.33 0.27 0.27 0.61 0.37 0.30
TCTN2 ENST00000303372 79.21 54.37 68.83 0.33 0.61 0.46 0.61 1.68 1.05
OPTC ENST00000367222 79.22 88.62 87.10 0.33 0.24 0.28 0.60 0.35 0.30
SCGB1C1 ENST00000342878 79.22 92.83 89.14 0.33 0.29 0.19 0.60 0.30 0.25
TTLL6 ENST00000393382 79.23 59.33 71.87 0.33 0.51 0.44 0.60 1.41 0.82
GPR157 ENST00000377411 79.23 67.75 76.58 0.33 0.52 0.37 0.60 1.18 0.61
GINS2 ENST00000253462 79.24 89.63 87.57 0.33 0.27 0.27 0.60 0.36 0.31
ITGAX ENST00000268296 79.24 36.48 57.89 0.33 0.81 0.48 0.60 1.64 1.66
NKAIN4 ENST00000370316 79.25 56.37 70.05 0.33 0.52 0.47 0.59 1.53 0.91
FGF3 ENST00000334134 79.25 88.91 87.25 0.33 0.25 0.28 0.59 0.35 0.31
GTPBP3 ENST00000358792 79.26 69.10 77.35 0.33 0.56 0.35 0.59 1.14 0.58
C12orf55 ENST00000524981 79.26 40.34 60.23 0.33 0.61 0.47 0.59 1.74 1.60
TJP3 ENST00000589378 79.27 55.23 69.40 0.33 0.57 0.43 0.59 1.62 0.98
HIST1H4H ENST00000289352 79.27 97.03 91.09 0.33 0.24 0.15 0.59 0.19 0.20
LCN15 ENST00000316144 79.28 65.21 75.15 0.33 0.51 0.38 0.59 1.24 0.67
CCDC86 ENST00000227520 79.28 61.34 73.06 0.33 0.54 0.42 0.59 1.40 0.80

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