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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
KCNK17 ENST00000373231 80.97 80.99 84.29 0.32 0.35 0.34 0.60 0.56 0.41
C1QTNF9 ENST00000382071 80.97 71.86 79.71 0.32 0.51 0.38 0.60 1.07 0.53
DYNLT3 ENST00000378578 80.98 40.13 61.18 0.32 0.63 0.43 0.60 1.71 1.50
TMEM40 ENST00000314124 80.98 64.86 75.95 0.32 0.48 0.38 0.60 1.24 0.62
ZNF92 ENST00000328747 80.99 90.34 88.76 0.32 0.25 0.19 0.60 0.38 0.28
IQCC ENST00000537469 80.99 64.17 75.55 0.32 0.49 0.37 0.60 1.20 0.64
DBNDD1 ENST00000304733 81.00 81.30 84.50 0.32 0.33 0.33 0.60 0.54 0.40
RNASEH2C ENST00000308418 81.00 78.36 83.05 0.32 0.43 0.30 0.60 0.74 0.40
ITFG3 ENST00000399932 81.01 70.32 78.96 0.32 0.52 0.39 0.60 1.10 0.52
LRPAP1 ENST00000500728 81.01 63.86 75.35 0.32 0.49 0.37 0.60 1.20 0.65
OR6C3 ENST00000379667 81.02 84.24 85.92 0.32 0.28 0.33 0.60 0.44 0.33
IL8 ENST00000307407 81.02 92.36 89.78 0.32 0.25 0.18 0.60 0.30 0.23
ATF4 ENST00000337304 81.03 61.48 74.06 0.32 0.54 0.38 0.60 1.40 0.69
PDIA2 ENST00000219406 81.03 97.14 91.84 0.32 0.24 0.14 0.60 0.18 0.17
ZP1 ENST00000278853 81.04 71.18 79.38 0.32 0.52 0.39 0.60 1.07 0.52
PIP5KL1 ENST00000388747 81.04 53.86 69.66 0.32 0.63 0.44 0.60 1.70 0.95
UNKL ENST00000389221 81.05 18.29 48.58 0.32 1.51 0.67 0.60 0.74 1.85
GLT1D1 ENST00000281703 81.05 75.41 81.62 0.32 0.46 0.37 0.60 0.90 0.47
PER3 ENST00000361923 81.06 45.21 64.44 0.32 0.70 0.51 0.60 1.98 1.34
MT1G ENST00000444837 81.07 90.96 89.11 0.32 0.25 0.19 0.60 0.35 0.26
CBWD1 ENST00000356521 81.07 63.59 75.23 0.32 0.51 0.37 0.60 1.25 0.67
POU5F1B ENST00000465342 81.08 89.78 88.54 0.32 0.27 0.22 0.60 0.37 0.28
BTNL9 ENST00000327705 81.08 71.16 79.40 0.32 0.52 0.39 0.60 1.06 0.52
CD3D ENST00000300692 81.09 78.15 82.97 0.32 0.42 0.32 0.60 0.73 0.40
SPTBN5 ENST00000320955 81.09 56.13 71.00 0.32 0.52 0.43 0.60 1.55 0.85

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