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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
KRTAP13-2 ENST00000399889 83.68 96.60 92.89 0.29 0.23 0.14 0.51 0.20 0.15
CYP2B6 ENST00000324071 83.68 66.04 78.06 0.29 0.56 0.39 0.52 1.21 0.55
TXNDC8 ENST00000374510 83.69 56.27 72.67 0.29 0.52 0.43 0.52 1.55 0.81
SYNE4 ENST00000324444 83.69 71.09 80.70 0.29 0.49 0.39 0.52 1.07 0.52
TNFRSF17 ENST00000053243 83.70 92.74 91.18 0.29 0.29 0.15 0.52 0.30 0.18
MXD3 ENST00000439742 83.70 67.13 78.69 0.30 0.54 0.38 0.51 1.22 0.54
C2orf88 ENST00000340623 83.71 96.23 92.72 0.30 0.22 0.14 0.50 0.19 0.15
CDCA4 ENST00000336219 83.71 74.11 82.27 0.30 0.53 0.34 0.50 1.03 0.45
ZNF446 ENST00000594369 83.72 62.56 76.22 0.30 0.52 0.37 0.50 1.31 0.62
MPG ENST00000219431 83.73 83.80 86.95 0.30 0.27 0.28 0.50 0.47 0.30
KCNK18 ENST00000334549 83.73 60.95 75.22 0.30 0.54 0.37 0.50 1.41 0.67
EDN3 ENST00000337938 83.74 51.44 69.81 0.30 0.63 0.44 0.50 1.89 0.93
PCDHB10 ENST00000239446 83.74 53.92 71.31 0.30 0.65 0.43 0.50 1.70 0.87
KLK5 ENST00000336334 83.75 53.81 71.24 0.30 0.63 0.44 0.50 1.71 0.86
NLRP10 ENST00000328600 83.75 78.93 84.68 0.29 0.40 0.34 0.50 0.69 0.40
FAM92B ENST00000539556 83.76 80.64 85.55 0.29 0.37 0.33 0.50 0.57 0.35
KLHDC4 ENST00000270583 83.76 91.36 90.63 0.29 0.23 0.15 0.50 0.34 0.20
CYP4F11 ENST00000402119 83.77 82.37 86.28 0.29 0.34 0.33 0.50 0.52 0.33
ZNF431 ENST00000311048 83.77 54.34 71.58 0.29 0.62 0.44 0.50 1.68 0.83
MTMR8 ENST00000374852 83.78 92.31 90.99 0.29 0.25 0.15 0.49 0.30 0.20
KLF17 ENST00000372299 83.78 73.15 81.83 0.29 0.53 0.37 0.49 1.02 0.47
LGALS3BP ENST00000262776 83.79 76.81 83.70 0.29 0.42 0.34 0.49 0.81 0.40
ATP5D ENST00000215375 83.79 78.46 84.47 0.29 0.43 0.33 0.49 0.74 0.40
NMS ENST00000376865 83.80 81.76 86.02 0.29 0.33 0.33 0.49 0.51 0.33
CLRN3 ENST00000368671 83.80 65.97 78.09 0.29 0.56 0.39 0.49 1.23 0.55

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