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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
STOML1 ENST00000316900 47.27 77.51 63.57 0.56 0.42 0.49 1.83 0.78 1.40
MRVI1 ENST00000423302 47.27 31.38 37.60 0.56 0.97 0.84 1.83 1.41 2.01
NT5E ENST00000257770 47.28 63.68 55.06 0.56 0.49 0.51 1.83 1.23 1.74
FAM171A1 ENST00000378116 47.28 13.00 28.32 0.56 2.09 0.78 1.83 0.59 1.28
CNGA2 ENST00000329903 47.29 40.83 42.32 0.56 0.61 0.70 1.83 1.78 2.01
PDIA4 ENST00000286091 47.29 25.48 34.59 0.56 1.25 0.90 1.83 1.06 1.77
APLP1 ENST00000221891 47.30 21.00 32.35 0.56 1.44 0.91 1.83 0.83 1.61
COQ5 ENST00000288532 47.30 50.81 47.91 0.56 0.63 0.66 1.82 1.93 1.89
GSTCD ENST00000515279 47.31 44.57 44.45 0.56 0.65 0.61 1.82 1.97 2.04
MARS2 ENST00000282276 47.31 45.94 45.32 0.56 0.76 0.70 1.82 2.02 2.01
PDK4 ENST00000005178 47.32 70.12 58.81 0.56 0.53 0.51 1.82 1.12 1.65
SMPDL3A ENST00000368440 47.32 89.77 70.91 0.56 0.27 0.43 1.82 0.37 0.86
AKAP13 ENST00000361243 47.33 11.86 27.75 0.56 2.09 0.90 1.81 0.58 1.27
FAM129B ENST00000373312 47.33 22.01 32.83 0.56 1.48 0.85 1.81 0.81 1.65
MRS2 ENST00000378386 47.34 54.74 50.03 0.56 0.58 0.61 1.82 1.63 1.92
IRGC ENST00000244314 47.34 44.47 44.40 0.56 0.63 0.59 1.82 1.98 2.03
GLTP ENST00000318348 47.35 45.58 45.13 0.56 0.75 0.70 1.82 1.99 2.00
IL22 ENST00000538666 47.35 83.97 67.46 0.56 0.28 0.52 1.82 0.46 1.14
PAK6 ENST00000560346 47.36 38.11 40.94 0.56 0.77 0.78 1.82 1.70 2.06
CENPW ENST00000368328 47.36 50.19 47.55 0.56 0.67 0.65 1.83 1.99 1.89
HRSP12 ENST00000254878 47.37 56.21 50.84 0.56 0.52 0.67 1.82 1.56 1.85
TUBGCP2 ENST00000543663 47.37 34.33 39.23 0.56 0.82 0.77 1.82 1.56 2.04
TRAPPC5 ENST00000317378 47.38 78.09 64.01 0.56 0.43 0.52 1.82 0.74 1.39
TBC1D2 ENST00000375066 47.38 44.23 44.28 0.56 0.62 0.61 1.82 1.95 2.05
C20orf195 ENST00000370098 47.39 76.17 62.71 0.56 0.43 0.49 1.82 0.87 1.39

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