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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
WFDC11 ENST00000356562 98.73 86.59 95.42 0.10 0.24 0.08 0.11 0.40 0.11
PRAMEF13 ENST00000376132 94.95 93.55 97.01 0.10 0.28 0.08 0.12 0.28 0.07
SAA2 ENST00000526900 88.96 96.37 95.41 0.19 0.22 0.08 0.32 0.19 0.11
RP11-67H2.1 ENST00000521500 92.27 96.63 97.01 0.15 0.23 0.08 0.18 0.20 0.07
C22orf42 ENST00000382097 95.94 89.38 95.41 0.11 0.27 0.08 0.11 0.37 0.11
GOLGA6L10 ENST00000439287 93.17 95.05 97.00 0.15 0.23 0.08 0.16 0.21 0.07
WFDC12 ENST00000372785 99.13 86.16 95.40 0.11 0.27 0.08 0.12 0.42 0.11
OR2T8 ENST00000319968 89.31 99.00 97.00 0.18 0.15 0.08 0.32 0.15 0.07
RFPL1 ENST00000354373 97.68 87.62 95.40 0.10 0.23 0.08 0.10 0.35 0.11
RP11-404L6.2 ENST00000520762 92.91 92.08 95.39 0.16 0.24 0.08 0.16 0.32 0.11
AC004899.1 ENST00000596947 89.32 98.97 96.99 0.18 0.17 0.08 0.32 0.15 0.07
C1orf147 ENST00000367119 93.08 95.26 95.39 0.15 0.23 0.08 0.15 0.21 0.10
ZNF665 ENST00000396424 98.44 90.02 96.99 0.10 0.25 0.08 0.11 0.37 0.07
IFI27L2 ENST00000238609 89.29 95.97 95.38 0.18 0.22 0.08 0.32 0.20 0.10
TAS2R16 ENST00000249284 88.84 99.52 96.98 0.19 0.16 0.08 0.32 0.13 0.07
RNF222 ENST00000399398 92.40 92.47 95.38 0.15 0.27 0.08 0.18 0.30 0.10
AL033381.1 ENST00000314040 91.20 96.19 96.98 0.15 0.22 0.08 0.21 0.20 0.07
CCRL2 ENST00000357392 96.40 88.86 95.37 0.10 0.25 0.08 0.11 0.35 0.10
AC006132.1 ENST00000593161 92.71 96.85 96.97 0.15 0.23 0.08 0.17 0.19 0.07
C8orf86 ENST00000358138 98.31 86.94 95.37 0.09 0.22 0.08 0.10 0.40 0.10
DEFB107A ENST00000335021 93.64 91.47 95.36 0.13 0.23 0.08 0.13 0.32 0.10
WFDC10B ENST00000335769 99.68 88.71 96.97 0.12 0.25 0.08 0.13 0.35 0.07
RBMY1A1 ENST00000382707 91.18 93.58 95.36 0.15 0.28 0.08 0.21 0.28 0.10
BX088651.1 ENST00000540551 89.52 98.61 96.96 0.16 0.20 0.08 0.30 0.15 0.07
CCL23 ENST00000293280 99.23 86.00 95.35 0.11 0.27 0.08 0.12 0.43 0.10

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