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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
DUSP13 ENST00000372700 60.31 71.42 67.72 0.61 0.53 0.52 1.39 1.06 1.12
LRPPRC ENST00000260665 60.31 27.46 42.12 0.61 1.25 0.71 1.39 1.16 1.99
OTOA ENST00000388958 60.32 36.54 47.19 0.61 0.78 0.67 1.38 1.63 1.89
LGALS12 ENST00000340246 60.32 84.16 75.17 0.61 0.27 0.38 1.38 0.44 0.67
WRAP73 ENST00000270708 60.33 42.37 50.40 0.61 0.59 0.67 1.38 1.90 1.90
C9orf64 ENST00000376344 60.33 68.35 65.97 0.61 0.52 0.51 1.38 1.21 1.24
CISD1 ENST00000333926 60.34 77.53 71.45 0.61 0.42 0.46 1.38 0.79 0.86
FNDC8 ENST00000158009 60.34 71.26 67.65 0.61 0.53 0.51 1.38 1.07 1.13
LCTL ENST00000341509 60.35 70.13 66.98 0.61 0.53 0.53 1.38 1.11 1.19
SLC39A3 ENST00000269740 60.35 63.60 63.04 0.61 0.51 0.51 1.38 1.24 1.39
NPSR1 ENST00000359791 60.36 66.46 64.78 0.59 0.56 0.51 1.38 1.20 1.32
USH2A ENST00000307340 60.36 44.96 51.83 0.59 0.68 0.62 1.39 1.97 1.92
KRT34 ENST00000394001 60.37 62.62 62.32 0.59 0.51 0.48 1.39 1.31 1.41
SPG7 ENST00000268704 60.37 82.85 74.54 0.59 0.32 0.40 1.39 0.49 0.69
CHCHD7 ENST00000303759 60.38 66.58 64.88 0.59 0.54 0.51 1.38 1.22 1.33
GRPEL1 ENST00000264954 60.38 40.60 49.36 0.59 0.63 0.71 1.38 1.77 1.84
MRPL42 ENST00000549982 60.39 65.47 64.21 0.59 0.54 0.51 1.38 1.24 1.35
AVPR1A ENST00000299178 60.39 66.02 64.55 0.59 0.56 0.51 1.38 1.22 1.33
WDR88 ENST00000355868 60.40 62.17 62.08 0.59 0.53 0.48 1.38 1.35 1.45
SMOC2 ENST00000354536 60.40 31.74 44.64 0.59 0.95 0.62 1.38 1.48 2.06
THOP1 ENST00000307741 60.41 32.78 45.30 0.59 0.84 0.70 1.38 1.44 2.01
STX2 ENST00000392373 60.42 60.77 61.27 0.59 0.56 0.44 1.38 1.39 1.48
ACBD4 ENST00000431281 60.42 49.10 54.30 0.59 0.66 0.59 1.37 2.04 1.73
DEGS2 ENST00000305631 60.43 61.39 61.63 0.59 0.54 0.46 1.37 1.40 1.47
XPNPEP2 ENST00000371106 60.43 60.56 61.09 0.58 0.52 0.43 1.37 1.41 1.53

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