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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
CALY ENST00000252939 67.93 65.55 68.76 0.58 0.53 0.46 1.03 1.22 1.06
LCNL1 ENST00000408973 67.93 92.93 83.82 0.58 0.29 0.34 1.03 0.30 0.42
ZNF215 ENST00000278319 67.94 72.16 72.75 0.58 0.52 0.43 1.03 1.04 0.82
OR10G2 ENST00000542433 67.94 85.09 79.85 0.58 0.25 0.37 1.03 0.45 0.52
BCL3 ENST00000164227 67.95 7.04 35.64 0.58 2.57 0.85 1.03 0.37 1.77
EIF4EBP2 ENST00000373218 67.95 75.57 74.68 0.58 0.44 0.40 1.03 0.90 0.67
SLC26A10 ENST00000320442 67.96 73.63 73.59 0.58 0.52 0.40 1.03 1.03 0.74
ARMC10 ENST00000323716 67.96 65.13 68.52 0.58 0.49 0.47 1.03 1.24 1.06
VSTM5 ENST00000409977 67.97 89.53 82.12 0.58 0.27 0.35 1.03 0.36 0.46
GAS8 ENST00000268699 67.97 65.32 68.66 0.58 0.51 0.47 1.03 1.25 1.05
CCDC82 ENST00000278520 67.98 44.44 55.88 0.58 0.62 0.49 1.03 1.97 1.76
KRT83 ENST00000293670 67.98 76.19 75.02 0.58 0.43 0.39 1.03 0.86 0.66
IFIT2 ENST00000371826 67.99 44.53 55.94 0.58 0.65 0.49 1.03 1.97 1.76
ZCCHC18 ENST00000537356 67.99 50.89 59.81 0.58 0.63 0.49 1.03 1.92 1.63
EFCAB2 ENST00000366523 68.00 81.59 77.98 0.58 0.33 0.38 1.03 0.52 0.54
LCMT2 ENST00000305641 68.00 77.50 75.76 0.58 0.42 0.38 1.03 0.78 0.64
UQCR10 ENST00000330029 68.01 88.28 81.49 0.58 0.23 0.35 1.03 0.37 0.48
ASIC5 ENST00000537611 68.01 72.00 72.71 0.58 0.51 0.43 1.03 1.05 0.81
PCDHGA5 ENST00000518069 68.02 52.34 60.77 0.58 0.62 0.44 1.03 1.81 1.61
CCL27 ENST00000259631 68.02 84.61 79.57 0.58 0.28 0.38 1.03 0.42 0.52
KRT74 ENST00000305620 68.03 81.78 78.13 0.58 0.34 0.39 1.03 0.51 0.55
GPR179 ENST00000342292 68.03 45.98 56.86 0.58 0.77 0.52 1.03 2.02 1.70
PPP1R26 ENST00000356818 68.04 98.45 86.80 0.57 0.21 0.29 1.03 0.14 0.32
GAA ENST00000302262 68.04 52.70 60.98 0.57 0.67 0.43 1.03 1.80 1.58
ASB12 ENST00000362002 68.05 87.55 81.15 0.57 0.23 0.39 1.03 0.37 0.49

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