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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
AKR1A1 ENST00000372070 32.67 60.47 45.29 0.95 0.52 0.70 1.70 1.41 2.01
TAGLN2 ENST00000368097 32.68 52.14 40.60 0.95 0.62 0.81 1.70 1.85 2.04
EPG5 ENST00000282041 32.68 22.04 25.44 0.95 1.48 1.02 1.70 0.81 1.18
ANXA8L1 ENST00000359178 32.69 90.63 62.52 0.95 0.25 0.48 1.70 0.37 1.39
DPF3 ENST00000541685 32.69 33.08 31.08 0.94 0.84 0.84 1.70 1.49 1.52
POMGNT1 ENST00000371992 32.70 57.26 43.34 0.94 0.56 0.63 1.70 1.50 2.00
HTT ENST00000355072 32.70 4.42 16.36 0.94 3.28 1.71 1.70 0.32 0.67
CCM2 ENST00000381112 32.71 34.50 31.82 0.94 0.80 0.90 1.70 1.56 1.58
EPS15 ENST00000371733 32.72 22.44 25.65 0.94 1.52 1.05 1.71 0.82 1.21
MYCL ENST00000397332 32.72 34.37 31.75 0.94 0.82 0.89 1.71 1.56 1.58
NEFM ENST00000221166 32.73 24.94 27.01 0.94 1.32 1.00 1.71 1.07 1.28
HIST2H2AB ENST00000331128 32.73 56.68 43.08 0.94 0.53 0.65 1.71 1.55 2.01
SSX2IP ENST00000342203 32.74 43.26 36.11 0.94 0.62 0.89 1.71 1.92 1.80
SNX16 ENST00000396330 32.74 84.02 58.43 0.94 0.27 0.52 1.71 0.45 1.65
RPL7A ENST00000323345 32.75 5.02 16.73 0.95 3.24 1.68 1.71 0.32 0.70
SACS ENST00000382298 32.75 27.26 28.19 0.95 1.25 0.82 1.71 1.15 1.28
SAFB ENST00000588852 32.76 2.82 15.62 0.95 3.51 1.76 1.71 0.28 0.67
HARS ENST00000504156 32.76 41.81 35.48 0.95 0.61 0.87 1.71 1.80 1.78
PRDM12 ENST00000253008 32.77 17.20 23.10 0.95 1.59 1.20 1.71 0.75 1.00
IPMK ENST00000373935 32.77 15.03 22.02 0.95 1.91 1.16 1.70 0.64 0.97
ARHGAP19-SLIT1 ENST00000453547 32.78 52.71 40.96 0.95 0.67 0.77 1.70 1.80 2.05
PRPSAP1 ENST00000446526 32.78 67.28 48.92 0.95 0.56 0.71 1.70 1.21 1.84
NPL ENST00000367553 32.79 62.53 46.31 0.95 0.53 0.67 1.70 1.31 1.91
ARL2BP ENST00000219204 32.79 74.19 52.79 0.94 0.53 0.61 1.70 1.02 1.88
SNX1 ENST00000261889 32.80 16.02 22.61 0.94 1.85 1.18 1.70 0.67 0.96

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