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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
CLECL1 ENST00000327839 94.65 74.72 87.80 0.10 0.54 0.24 0.11 0.96 0.32
MADCAM1 ENST00000215637 94.66 42.73 71.15 0.10 0.62 0.43 0.11 1.92 0.87
IFI30 ENST00000407280 94.66 79.47 90.13 0.10 0.38 0.18 0.11 0.66 0.21
OR4F4 ENST00000326183 94.67 92.66 96.41 0.10 0.29 0.07 0.11 0.31 0.09
NBPF12 ENST00000442909 94.67 92.89 96.58 0.10 0.29 0.08 0.11 0.30 0.07
FAM9B ENST00000327220 94.68 86.13 93.17 0.10 0.27 0.14 0.11 0.42 0.15
WHAMM ENST00000286760 94.69 58.34 79.84 0.10 0.54 0.38 0.11 1.41 0.52
NDUFA3 ENST00000485876 94.69 78.15 89.56 0.10 0.42 0.18 0.11 0.73 0.23
NBPF6 ENST00000444143 94.70 86.46 93.28 0.10 0.24 0.13 0.11 0.42 0.15
KRTAP12-2 ENST00000360770 94.70 97.96 98.57 0.10 0.20 0.10 0.11 0.17 0.05
LY6D ENST00000301263 94.71 93.15 96.70 0.10 0.28 0.08 0.11 0.30 0.08
ZNF627 ENST00000361113 94.71 59.57 80.48 0.10 0.52 0.39 0.11 1.41 0.50
POTEF ENST00000357462 94.72 56.40 78.79 0.10 0.52 0.39 0.11 1.53 0.52
ZNF419 ENST00000424930 94.72 84.46 92.27 0.10 0.29 0.14 0.11 0.44 0.15
CXorf61 ENST00000371894 94.73 94.27 97.21 0.10 0.24 0.08 0.11 0.25 0.06
MAGEB2 ENST00000378988 94.73 97.71 98.49 0.10 0.21 0.10 0.11 0.17 0.05
OR6F1 ENST00000302084 94.74 95.84 97.83 0.10 0.22 0.09 0.11 0.20 0.04
C10orf91 ENST00000392630 94.74 90.48 95.34 0.10 0.25 0.08 0.11 0.37 0.10
C16orf96 ENST00000444310 94.75 59.14 80.27 0.10 0.49 0.38 0.11 1.44 0.51
CDRT15 ENST00000420162 94.75 91.15 95.73 0.10 0.24 0.07 0.11 0.35 0.11
CLEC10A ENST00000254868 94.76 64.41 82.92 0.10 0.48 0.32 0.11 1.22 0.40
OR5D13 ENST00000361760 94.76 97.55 98.43 0.10 0.22 0.10 0.11 0.19 0.05
IFNA2 ENST00000380206 94.77 99.71 98.97 0.10 0.17 0.10 0.11 0.11 0.04
CRISP1 ENST00000335847 94.77 76.22 88.63 0.10 0.43 0.22 0.11 0.85 0.28
IL36G ENST00000259205 94.78 83.01 91.72 0.10 0.32 0.14 0.11 0.49 0.18

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