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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
RIPK3 ENST00000216274 83.55 74.59 82.47 0.30 0.53 0.33 0.52 0.99 0.44
TMEM52 ENST00000310991 83.55 84.91 87.40 0.30 0.27 0.28 0.52 0.44 0.31
HIGD2B ENST00000311755 83.56 98.36 93.83 0.30 0.21 0.10 0.52 0.14 0.13
NHLH2 ENST00000369506 83.56 63.78 76.80 0.29 0.49 0.35 0.52 1.22 0.61
CXCL3 ENST00000296026 83.57 91.43 90.57 0.29 0.23 0.15 0.51 0.33 0.21
TRIM52 ENST00000327767 83.58 86.52 88.21 0.29 0.24 0.23 0.51 0.42 0.30
AKR1C4 ENST00000380448 83.58 87.37 88.59 0.29 0.23 0.22 0.51 0.41 0.28
CLEC2B ENST00000228438 83.59 66.09 78.03 0.29 0.54 0.38 0.51 1.20 0.54
GALNT8 ENST00000252318 83.59 75.17 82.77 0.29 0.49 0.32 0.52 0.91 0.42
AC103809.2 ENST00000599136 83.60 89.16 89.51 0.29 0.27 0.18 0.52 0.35 0.23
FAM110C ENST00000327669 83.60 89.37 89.63 0.29 0.27 0.18 0.52 0.37 0.23
ANKMY1 ENST00000391987 83.61 64.10 76.99 0.29 0.49 0.37 0.52 1.20 0.61
OAZ1 ENST00000602676 83.61 37.75 61.36 0.29 0.80 0.44 0.52 1.70 1.48
GSTA5 ENST00000370989 83.62 94.77 91.95 0.29 0.23 0.14 0.52 0.24 0.16
STEAP1B ENST00000404369 83.62 71.48 80.89 0.29 0.53 0.39 0.52 1.05 0.51
HIST1H1E ENST00000304218 83.63 83.16 86.59 0.29 0.29 0.30 0.52 0.48 0.33
IFNA21 ENST00000380225 83.63 99.81 94.47 0.29 0.17 0.10 0.52 0.11 0.12
ADH6 ENST00000394899 83.64 61.18 75.33 0.29 0.53 0.37 0.52 1.39 0.65
SPP1 ENST00000395080 83.64 86.81 88.38 0.29 0.23 0.22 0.52 0.40 0.30
PGPEP1L ENST00000378919 83.65 96.82 92.98 0.29 0.23 0.14 0.52 0.19 0.15
SPRR2E ENST00000368751 83.65 96.16 92.65 0.29 0.21 0.14 0.52 0.20 0.15
C10orf90 ENST00000284694 83.66 69.68 80.01 0.29 0.53 0.35 0.52 1.12 0.52
TCHHL1 ENST00000368806 83.66 59.41 74.45 0.29 0.51 0.40 0.52 1.41 0.69
KRTAP12-1 ENST00000391617 83.67 99.30 94.33 0.29 0.16 0.10 0.52 0.12 0.12
ZACN ENST00000334586 83.67 95.91 92.52 0.29 0.22 0.14 0.52 0.20 0.15

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