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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
DEFB121 ENST00000376314 98.43 93.79 98.39 0.10 0.27 0.10 0.11 0.26 0.05
MUC5B ENST00000529681 97.12 8.18 51.80 0.10 2.57 0.62 0.11 0.44 1.92
STATH ENST00000246895 98.43 89.50 96.79 0.10 0.27 0.08 0.11 0.36 0.08
ZNF224 ENST00000336976 97.12 84.84 93.78 0.10 0.27 0.10 0.11 0.42 0.13
ZNF665 ENST00000396424 98.44 90.02 96.99 0.10 0.25 0.08 0.11 0.37 0.07
BIK ENST00000216115 97.13 94.52 98.18 0.10 0.23 0.09 0.11 0.24 0.05
NUTM2B ENST00000429828 97.13 75.33 89.33 0.10 0.49 0.18 0.11 0.90 0.25
OR7C1 ENST00000248073 98.45 97.99 99.60 0.10 0.20 0.12 0.11 0.17 0.05
ZDHHC11B ENST00000508859 97.14 83.36 93.00 0.10 0.27 0.14 0.11 0.48 0.15
FMR1NB ENST00000370467 98.45 48.03 76.35 0.10 0.63 0.35 0.11 2.00 0.61
C16orf91 ENST00000310355 97.14 89.35 95.98 0.10 0.27 0.07 0.11 0.37 0.10
C7orf69 ENST00000258776 98.46 91.39 97.52 0.10 0.23 0.08 0.11 0.33 0.07
PILRB ENST00000610247 97.15 73.95 88.68 0.10 0.53 0.20 0.11 1.02 0.28
DPPA3 ENST00000345088 98.46 46.98 75.72 0.10 0.71 0.38 0.11 1.95 0.64
ADAM29 ENST00000359240 97.15 98.85 99.55 0.10 0.16 0.12 0.11 0.14 0.05
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
ZNF676 ENST00000397121 97.16 82.41 92.51 0.10 0.34 0.14 0.11 0.52 0.15
CFHR2 ENST00000367415 97.16 90.42 96.57 0.10 0.25 0.08 0.11 0.37 0.07
RAET1G ENST00000367360 98.47 76.00 90.27 0.10 0.43 0.16 0.11 0.86 0.22
PRSS38 ENST00000366757 97.17 68.29 85.96 0.10 0.52 0.33 0.11 1.20 0.33
IVL ENST00000368764 98.48 99.18 99.85 0.10 0.15 0.12 0.11 0.13 0.04
UGT2B4 ENST00000305107 97.17 68.96 86.29 0.10 0.54 0.33 0.11 1.15 0.33
OR14A16 ENST00000357627 98.48 99.12 99.68 0.10 0.15 0.12 0.11 0.14 0.04
ORM1 ENST00000259396 97.18 66.69 85.29 0.10 0.56 0.34 0.11 1.22 0.36
GSDMD ENST00000526406 98.49 75.44 90.06 0.10 0.46 0.18 0.11 0.90 0.22

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