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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
KLHL42 ENST00000381271 29.96 38.18 32.26 1.08 0.77 0.90 1.59 1.71 1.61
ATP6V1C2 ENST00000272238 29.97 51.50 39.07 1.09 0.63 0.77 1.59 1.87 2.06
LPCAT1 ENST00000283415 29.97 20.38 23.26 1.09 1.44 1.19 1.60 0.76 1.01
MYL6 ENST00000550697 29.98 71.27 49.56 1.09 0.53 0.67 1.60 1.07 1.85
ZFHX3 ENST00000268489 29.98 2.37 13.84 1.09 3.63 2.10 1.59 0.29 0.57
GALNT4 ENST00000529983 29.99 25.00 25.58 1.09 1.33 1.05 1.59 1.05 1.20
MDH1 ENST00000539945 29.99 17.03 21.65 1.09 1.62 1.27 1.59 0.73 0.91
PDLIM1 ENST00000329399 30.00 43.95 35.14 1.09 0.61 0.86 1.59 1.97 1.76
GRAP2 ENST00000344138 30.00 38.37 32.39 1.09 0.75 0.91 1.59 1.72 1.61
MED20 ENST00000265350 30.01 39.33 32.84 1.09 0.70 0.85 1.59 1.64 1.65
VPS13B ENST00000358544 30.01 33.19 29.76 1.08 0.82 0.86 1.59 1.50 1.42
CNTN2 ENST00000331830 30.02 20.91 23.57 1.08 1.43 1.19 1.60 0.83 1.01
TRAK2 ENST00000332624 30.02 43.46 34.89 1.08 0.61 0.90 1.60 1.95 1.76
RBM4B ENST00000525754 30.03 40.93 33.64 1.08 0.61 0.90 1.60 1.78 1.72
XIAP ENST00000371199 30.03 16.38 21.32 1.08 1.80 1.38 1.60 0.69 0.91
DIRC2 ENST00000261038 30.04 63.08 45.26 1.08 0.48 0.70 1.60 1.29 2.00
TTC26 ENST00000464848 30.04 38.07 32.26 1.08 0.77 0.90 1.60 1.70 1.61
TRPV1 ENST00000571088 30.05 60.17 43.51 1.06 0.52 0.62 1.60 1.38 1.99
SHPK ENST00000572705 30.06 60.21 43.53 1.06 0.52 0.62 1.60 1.39 2.00
LMBRD1 ENST00000370577 30.06 49.73 38.14 1.05 0.66 0.86 1.60 2.03 2.04
ADAMTS19 ENST00000274487 30.07 27.92 27.15 1.05 1.20 0.99 1.59 1.19 1.25
PCBD1 ENST00000299299 30.07 89.86 60.45 1.05 0.27 0.44 1.59 0.37 1.58
RAB3GAP1 ENST00000442034 30.08 28.21 27.28 1.05 1.18 0.97 1.59 1.22 1.25
TAP1 ENST00000354258 30.08 34.34 30.42 1.05 0.82 0.80 1.60 1.56 1.46
DNAJB11 ENST00000439351 30.09 26.64 26.46 1.05 1.20 1.00 1.60 1.12 1.25

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