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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
ZNF763 ENST00000343949 97.48 79.79 91.51 0.10 0.35 0.15 0.11 0.62 0.18
ANKRD62 ENST00000587848 98.06 17.82 58.00 0.11 1.52 0.47 0.11 0.72 1.68
CSN1S1 ENST00000246891 98.64 87.96 96.03 0.10 0.25 0.07 0.11 0.37 0.11
SPATA31A1 ENST00000377647 96.33 89.07 95.47 0.12 0.27 0.08 0.11 0.35 0.11
PRR23B ENST00000329447 96.91 98.57 99.42 0.09 0.20 0.11 0.11 0.15 0.05
GSTT2B ENST00000290765 97.49 39.24 70.68 0.10 0.70 0.43 0.11 1.64 0.88
MAGEB1 ENST00000378981 98.07 97.72 99.47 0.11 0.21 0.11 0.11 0.17 0.05
OR14I1 ENST00000342623 98.65 98.02 99.65 0.10 0.20 0.12 0.11 0.16 0.04
ZNF43 ENST00000354959 95.76 88.54 94.92 0.11 0.24 0.09 0.11 0.36 0.11
PRAMEF11 ENST00000535591 96.34 70.34 86.55 0.12 0.52 0.30 0.11 1.08 0.33
ZNF155 ENST00000407951 96.92 95.45 98.45 0.09 0.24 0.10 0.11 0.20 0.05
LRRC37A2 ENST00000576629 97.49 46.30 74.81 0.10 0.73 0.39 0.11 2.05 0.66
ZNF480 ENST00000595962 98.07 67.70 86.13 0.11 0.53 0.33 0.11 1.19 0.33
FAM194B ENST00000298738 98.65 59.53 82.46 0.10 0.49 0.33 0.11 1.41 0.44
CRLF2 ENST00000381567 95.76 76.01 89.01 0.11 0.44 0.19 0.11 0.86 0.27
IFNK ENST00000276943 96.34 93.50 97.53 0.10 0.28 0.08 0.11 0.28 0.07
TAS2R42 ENST00000334266 96.92 98.48 99.13 0.09 0.21 0.11 0.11 0.14 0.04
ZDHHC11 ENST00000283441 97.50 80.85 91.94 0.10 0.35 0.14 0.11 0.57 0.16
C10orf120 ENST00000329446 95.77 94.62 97.77 0.11 0.23 0.09 0.11 0.24 0.04
CTD-2215E18.1 ENST00000509481 98.08 93.54 98.17 0.11 0.28 0.09 0.11 0.28 0.05
SERPINB3 ENST00000283752 96.35 93.09 97.37 0.10 0.28 0.08 0.11 0.30 0.07
PILRA ENST00000198536 98.66 86.43 95.27 0.10 0.24 0.08 0.11 0.42 0.10
LILRB3 ENST00000245620 96.93 40.36 71.10 0.09 0.61 0.43 0.11 1.75 0.86
MAGEB6 ENST00000379034 97.51 98.03 99.40 0.10 0.20 0.11 0.11 0.16 0.04
PSG1 ENST00000244296 95.78 97.49 98.70 0.11 0.22 0.10 0.11 0.19 0.05

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