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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
ZNF860 ENST00000360311 86.91 99.73 95.70 0.24 0.17 0.07 0.39 0.11 0.11
OR5F1 ENST00000278409 86.91 97.04 94.70 0.24 0.24 0.09 0.39 0.19 0.11
MAP10 ENST00000418460 86.92 72.60 83.14 0.24 0.47 0.29 0.39 1.05 0.40
RMDN2 ENST00000234195 86.92 79.64 86.48 0.24 0.37 0.30 0.39 0.65 0.33
HSPB9 ENST00000355067 86.93 97.52 94.97 0.24 0.22 0.09 0.39 0.19 0.10
FAM132A ENST00000330388 86.93 84.50 88.84 0.24 0.29 0.19 0.39 0.43 0.28
TRMT44 ENST00000389737 86.94 75.31 84.48 0.24 0.49 0.33 0.39 0.90 0.40
ZNF100 ENST00000358296 86.94 83.03 88.15 0.24 0.32 0.23 0.39 0.49 0.30
OR7D2 ENST00000344248 86.95 98.70 95.71 0.24 0.18 0.07 0.39 0.15 0.11
ZNF780B ENST00000434248 86.95 83.89 88.53 0.24 0.28 0.22 0.39 0.46 0.28
KRTAP10-6 ENST00000400368 86.96 96.59 94.50 0.24 0.23 0.10 0.39 0.19 0.12
UGT2B10 ENST00000265403 86.96 83.70 88.48 0.24 0.27 0.22 0.39 0.48 0.29
PTGIR ENST00000291294 86.97 82.94 88.10 0.24 0.30 0.23 0.39 0.49 0.30
FAM174B ENST00000327355 86.97 91.20 91.85 0.24 0.23 0.14 0.39 0.35 0.17
FETUB ENST00000265029 86.98 69.93 81.82 0.23 0.53 0.37 0.39 1.14 0.46
ADAM8 ENST00000445355 86.98 47.80 69.57 0.23 0.59 0.44 0.39 1.99 0.95
NPPB ENST00000376468 86.99 92.51 92.44 0.23 0.29 0.14 0.39 0.31 0.15
FOXD4 ENST00000382500 86.99 92.44 92.40 0.23 0.27 0.14 0.39 0.30 0.15
GAL3ST2 ENST00000192314 87.00 93.15 92.79 0.23 0.28 0.14 0.39 0.30 0.15
UGT2B28 ENST00000335568 87.00 86.74 89.96 0.23 0.24 0.18 0.39 0.40 0.23
PINX1 ENST00000314787 87.01 87.83 90.48 0.23 0.24 0.14 0.39 0.38 0.21
PRAME ENST00000543184 87.02 72.40 83.07 0.23 0.51 0.30 0.39 1.03 0.40
RSPH10B2 ENST00000403107 87.02 28.90 58.00 0.23 1.15 0.47 0.39 1.31 1.68
PAGE4 ENST00000218068 87.03 41.40 65.83 0.23 0.62 0.51 0.39 1.80 1.25
RHD ENST00000328664 87.03 51.82 72.04 0.23 0.61 0.43 0.39 1.87 0.81

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