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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
RP11-404P21.8 ENST00000553811 98.29 93.96 98.40 0.09 0.25 0.10 0.10 0.26 0.05
C14orf132 ENST00000555004 92.66 99.13 98.40 0.15 0.15 0.10 0.18 0.14 0.05
AC016722.1 ENST00000409912 95.62 96.67 98.41 0.11 0.23 0.10 0.11 0.20 0.05
NUTM2A ENST00000381707 95.65 96.68 98.41 0.11 0.23 0.10 0.11 0.20 0.05
CT45A1 ENST00000497301 99.09 93.24 98.42 0.11 0.28 0.10 0.12 0.30 0.05
AF131215.5 ENST00000400102 91.06 98.24 98.42 0.16 0.21 0.10 0.21 0.15 0.05
OR5D13 ENST00000361760 94.76 97.55 98.43 0.10 0.22 0.10 0.11 0.19 0.05
PSG2 ENST00000406487 94.89 97.45 98.43 0.10 0.22 0.10 0.12 0.19 0.05
CXXC11 ENST00000343216 96.90 95.44 98.44 0.09 0.24 0.10 0.11 0.20 0.05
ZNF155 ENST00000407951 96.92 95.45 98.45 0.09 0.24 0.10 0.11 0.20 0.05
AC114546.1 ENST00000391457 92.73 99.17 98.45 0.15 0.15 0.10 0.17 0.14 0.05
PRAMEF17 ENST00000376098 95.71 96.74 98.46 0.11 0.23 0.10 0.12 0.19 0.05
FAM90A1 ENST00000538603 98.25 94.17 98.46 0.09 0.25 0.10 0.10 0.25 0.05
FAM106A ENST00000392176 92.79 99.21 98.47 0.15 0.15 0.10 0.17 0.13 0.05
ZNF846 ENST00000397902 96.86 95.66 98.47 0.09 0.23 0.10 0.11 0.20 0.05
C7orf13 ENST00000333319 93.52 99.62 98.48 0.13 0.16 0.10 0.14 0.12 0.05
OXCT2 ENST00000327582 95.51 96.98 98.48 0.11 0.24 0.10 0.11 0.19 0.05
MAGEB2 ENST00000378988 94.73 97.71 98.49 0.10 0.21 0.10 0.11 0.17 0.05
S100A7A ENST00000368729 96.23 96.30 98.49 0.12 0.22 0.10 0.11 0.19 0.05
AP000867.1 ENST00000343767 92.85 99.27 98.50 0.15 0.15 0.10 0.16 0.13 0.05
AC005477.1 ENST00000542853 93.42 99.56 98.50 0.13 0.16 0.10 0.15 0.12 0.05
PATE1 ENST00000305738 95.86 96.70 98.51 0.11 0.23 0.10 0.11 0.19 0.05
RP1L1 ENST00000382483 95.47 97.13 98.51 0.11 0.24 0.10 0.11 0.18 0.05
TBC1D3G ENST00000341264 92.92 99.29 98.52 0.16 0.16 0.10 0.16 0.12 0.05
MTRNR2L1 ENST00000540040 94.24 99.99 98.52 0.10 0.18 0.10 0.12 0.09 0.05

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