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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
KRTAP26-1 ENST00000360542 83.94 88.57 89.36 0.29 0.24 0.18 0.48 0.35 0.24
TMEM150B ENST00000326652 83.94 87.74 88.95 0.29 0.24 0.19 0.48 0.37 0.28
ERV3-1 ENST00000394323 83.95 98.41 94.06 0.29 0.21 0.09 0.48 0.14 0.12
C19orf60 ENST00000358607 83.95 78.00 84.27 0.29 0.42 0.34 0.48 0.77 0.42
NTN5 ENST00000270235 83.96 87.14 88.68 0.29 0.22 0.20 0.48 0.41 0.28
XCL2 ENST00000367819 83.96 88.60 89.39 0.29 0.24 0.18 0.48 0.35 0.24
ATAD3C ENST00000378785 83.97 64.72 77.58 0.29 0.48 0.37 0.48 1.24 0.57
GAL ENST00000265643 83.97 87.49 88.86 0.30 0.23 0.19 0.48 0.38 0.28
RNASE10 ENST00000328444 83.98 90.32 90.20 0.30 0.25 0.18 0.48 0.38 0.21
KRTAP10-3 ENST00000391620 83.98 75.97 83.35 0.30 0.43 0.33 0.48 0.86 0.40
DMKN ENST00000339686 83.99 58.31 73.94 0.30 0.54 0.40 0.48 1.43 0.70
MESP2 ENST00000341735 83.99 71.83 81.27 0.30 0.51 0.38 0.48 1.07 0.48
INMT ENST00000013222 84.00 85.90 88.09 0.30 0.28 0.23 0.48 0.43 0.30
OR2D3 ENST00000317834 84.00 70.66 80.65 0.30 0.51 0.39 0.47 1.09 0.51
KRTAP10-12 ENST00000400365 84.01 66.80 78.66 0.30 0.56 0.38 0.47 1.23 0.55
CCT8L2 ENST00000359963 84.01 82.35 86.37 0.30 0.34 0.33 0.47 0.52 0.33
FAM221B ENST00000423537 84.02 68.59 79.55 0.30 0.53 0.38 0.48 1.18 0.52
ACYP2 ENST00000394666 84.02 91.80 90.95 0.30 0.23 0.15 0.48 0.32 0.20
FAM115C ENST00000444908 84.03 94.78 92.09 0.30 0.23 0.14 0.48 0.24 0.16
MS4A7 ENST00000300184 84.03 80.00 85.38 0.30 0.37 0.34 0.48 0.61 0.35
FAM104B ENST00000425133 84.04 96.38 92.96 0.30 0.22 0.14 0.48 0.19 0.15
THAP3 ENST00000054650 84.05 67.17 78.86 0.30 0.54 0.39 0.48 1.22 0.52
OIP5 ENST00000220514 84.05 87.41 88.86 0.30 0.23 0.19 0.48 0.40 0.28
GLB1L3 ENST00000431683 84.06 63.31 76.81 0.30 0.47 0.35 0.48 1.31 0.61
PNMAL1 ENST00000313683 84.06 51.21 69.87 0.30 0.66 0.46 0.48 1.91 0.92

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