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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
ZNF639 ENST00000326361 21.05 46.95 32.22 1.53 0.71 0.91 1.02 1.95 1.60
REPS1 ENST00000258062 21.06 12.28 14.42 1.53 2.06 2.00 1.02 0.58 0.59
RASGRP2 ENST00000354024 21.06 22.96 20.07 1.54 1.47 1.49 1.02 0.90 0.86
ZNF768 ENST00000380412 21.07 24.66 21.00 1.53 1.29 1.43 1.02 1.05 0.88
NEK1 ENST00000507142 21.07 46.35 31.89 1.53 0.73 0.91 1.02 2.05 1.57
NUAK1 ENST00000261402 21.08 25.07 21.18 1.53 1.33 1.40 1.02 1.03 0.90
ACSL1 ENST00000515030 21.08 20.79 18.92 1.53 1.44 1.54 1.02 0.81 0.83
HMGN3 ENST00000344726 21.09 56.86 37.27 1.53 0.56 0.82 1.02 1.53 2.00
DSTYK ENST00000367162 21.09 14.91 15.82 1.53 1.94 1.77 1.02 0.62 0.66
POLR3F ENST00000377603 21.10 61.12 39.43 1.53 0.53 0.78 1.02 1.39 2.04
PRDM10 ENST00000358825 21.10 17.09 16.95 1.53 1.62 1.67 1.02 0.74 0.71
RACGAP1 ENST00000434422 21.11 25.53 21.45 1.53 1.25 1.30 1.02 1.05 0.91
MED12L ENST00000474524 21.11 4.58 10.43 1.53 3.24 2.18 1.02 0.32 0.43
APBB1 ENST00000299402 21.12 15.26 16.01 1.53 1.90 1.73 1.02 0.67 0.66
SETD3 ENST00000331768 21.12 22.87 20.06 1.53 1.47 1.49 1.02 0.90 0.86
DSTN ENST00000246069 21.13 38.00 27.72 1.53 0.77 0.92 1.02 1.71 1.27
ZFYVE9 ENST00000287727 21.14 12.87 14.77 1.53 2.07 1.96 1.02 0.59 0.62
SCAP ENST00000265565 21.14 25.14 21.25 1.53 1.32 1.39 1.02 1.03 0.90
ABCD1 ENST00000218104 21.15 3.09 9.58 1.53 3.46 2.28 1.02 0.28 0.40
IRF8 ENST00000268638 21.15 15.61 16.19 1.53 1.86 1.71 1.02 0.68 0.66
PDPK1 ENST00000342085 21.16 13.21 15.00 1.53 2.06 1.89 1.02 0.60 0.63
PAPSS1 ENST00000265174 21.16 39.80 28.65 1.53 0.65 0.80 1.02 1.68 1.34
BAZ2A ENST00000551812 21.17 2.34 9.22 1.53 3.64 2.32 1.02 0.29 0.38
ATF3 ENST00000341491 21.17 46.39 32.01 1.53 0.73 0.90 1.03 2.04 1.59
ATP5F1 ENST00000369722 21.18 46.73 32.15 1.53 0.73 0.91 1.03 1.97 1.59

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