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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
AMDHD1 ENST00000266736 57.21 63.88 61.16 0.56 0.49 0.43 1.57 1.21 1.51
AMER1 ENST00000330258 57.21 23.70 38.72 0.56 1.39 0.82 1.57 0.93 2.02
CYP39A1 ENST00000275016 57.22 74.58 67.79 0.56 0.53 0.51 1.57 1.00 1.12
OGDHL ENST00000374103 57.22 36.51 45.55 0.56 0.80 0.70 1.57 1.64 1.97
DDIT3 ENST00000551116 57.23 33.86 43.94 0.56 0.84 0.61 1.57 1.55 2.02
WBP5 ENST00000372661 57.23 90.13 76.80 0.56 0.25 0.35 1.57 0.38 0.61
STOML3 ENST00000379631 57.24 86.75 74.92 0.56 0.24 0.39 1.57 0.40 0.64
TCEA2 ENST00000343484 57.24 46.52 50.94 0.56 0.73 0.66 1.57 2.02 1.85
VPS37A ENST00000324849 57.25 37.45 46.05 0.56 0.76 0.68 1.57 1.66 1.97
IL7R ENST00000303115 57.25 56.62 56.76 0.56 0.53 0.52 1.57 1.55 1.70
MBOAT1 ENST00000324607 57.26 59.63 58.50 0.56 0.52 0.51 1.56 1.40 1.64
RNF166 ENST00000312838 57.26 32.26 43.13 0.56 0.86 0.65 1.56 1.46 1.99
PARP12 ENST00000263549 57.27 42.09 48.58 0.56 0.61 0.67 1.56 1.85 1.85
COL9A3 ENST00000343916 57.27 39.24 47.00 0.56 0.68 0.70 1.56 1.64 1.87
MRPS31 ENST00000323563 57.28 46.98 51.20 0.56 0.71 0.63 1.56 1.96 1.91
CALML3 ENST00000315238 57.29 93.95 78.88 0.56 0.25 0.39 1.56 0.26 0.52
SLCO1C1 ENST00000381552 57.29 54.76 55.72 0.56 0.58 0.53 1.56 1.63 1.74
NUP210 ENST00000254508 57.30 39.14 46.98 0.56 0.70 0.70 1.56 1.62 1.87
SLC30A8 ENST00000456015 57.30 77.39 69.52 0.56 0.42 0.44 1.56 0.76 0.96
CCK ENST00000396169 57.31 93.67 78.74 0.56 0.28 0.38 1.56 0.27 0.54
LRRCC1 ENST00000360375 57.31 52.83 54.66 0.56 0.65 0.56 1.57 1.80 1.73
PPIAL4G ENST00000419275 57.32 99.07 81.65 0.56 0.15 0.37 1.57 0.14 0.47
ANGPTL5 ENST00000334289 57.32 71.38 65.97 0.56 0.53 0.51 1.57 1.05 1.24
CIDEC ENST00000430427 57.33 51.92 54.11 0.56 0.61 0.59 1.57 1.85 1.75
CYP4V2 ENST00000378802 57.33 58.46 57.93 0.56 0.54 0.48 1.57 1.39 1.66

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