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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
KRTAP10-7 ENST00000380102 86.13 71.36 82.11 0.25 0.53 0.35 0.42 1.05 0.46
C1orf159 ENST00000421241 86.14 71.07 81.98 0.25 0.49 0.37 0.42 1.07 0.47
EFCAB4A ENST00000450448 86.14 86.24 89.30 0.25 0.27 0.19 0.42 0.43 0.25
C17orf99 ENST00000340363 86.15 44.17 66.88 0.25 0.61 0.53 0.42 1.95 1.20
ZNF788 ENST00000596883 86.15 85.60 88.99 0.25 0.27 0.19 0.42 0.44 0.27
OR5H15 ENST00000356526 86.16 97.09 94.39 0.25 0.24 0.10 0.42 0.19 0.12
OR5V1 ENST00000377154 86.16 84.71 88.55 0.25 0.27 0.22 0.42 0.42 0.28
TMEM155 ENST00000337677 86.17 89.12 90.69 0.25 0.27 0.15 0.42 0.35 0.20
FAM69C ENST00000343998 86.17 91.81 91.81 0.25 0.23 0.14 0.42 0.32 0.18
DNAAF1 ENST00000378553 86.18 55.89 73.79 0.25 0.51 0.42 0.42 1.56 0.71
SAA4 ENST00000278222 86.18 87.59 89.97 0.25 0.23 0.18 0.42 0.37 0.23
AREGB ENST00000380846 86.19 62.92 77.75 0.25 0.51 0.38 0.42 1.31 0.55
ADAMTSL5 ENST00000330475 86.19 63.46 78.02 0.25 0.49 0.38 0.42 1.25 0.54
OR7A17 ENST00000327462 86.20 92.00 91.87 0.25 0.23 0.14 0.42 0.33 0.17
SPAG11A ENST00000326558 86.20 94.47 93.08 0.25 0.23 0.14 0.42 0.24 0.15
OR5H14 ENST00000437310 86.21 96.08 93.88 0.25 0.21 0.09 0.42 0.20 0.11
MFSD12 ENST00000398558 86.21 74.39 83.69 0.25 0.53 0.34 0.42 1.00 0.40
RP11-389E17.1 ENST00000507870 86.22 90.80 91.40 0.25 0.25 0.15 0.42 0.35 0.18
PROSER2 ENST00000277570 86.22 83.81 88.17 0.25 0.27 0.23 0.42 0.47 0.30
OR2T10 ENST00000330500 86.23 95.32 93.53 0.25 0.24 0.13 0.42 0.21 0.15
DUXA ENST00000554048 86.24 78.61 85.73 0.25 0.40 0.33 0.42 0.74 0.33
GNRH2 ENST00000245983 86.24 95.06 93.34 0.25 0.23 0.13 0.42 0.21 0.15
OR2G6 ENST00000343414 86.25 87.98 90.17 0.25 0.25 0.18 0.42 0.37 0.21
C4orf51 ENST00000438731 86.25 76.78 84.89 0.25 0.40 0.34 0.42 0.82 0.40
CYP2C19 ENST00000371321 86.26 93.74 92.75 0.25 0.28 0.14 0.42 0.26 0.15

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