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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
PCP4 ENST00000328619 29.19 87.84 58.58 1.10 0.24 0.51 1.55 0.38 1.65
MYO18A ENST00000527372 29.19 11.78 18.43 1.10 2.09 1.62 1.55 0.57 0.81
FAM3A ENST00000447601 29.20 30.42 27.99 1.10 1.09 0.82 1.55 1.39 1.27
EPHA3 ENST00000336596 29.20 26.54 26.06 1.10 1.19 0.99 1.56 1.12 1.25
WIPI2 ENST00000288828 29.21 31.69 28.62 1.10 0.95 0.80 1.56 1.45 1.35
KLHL31 ENST00000370905 29.21 50.49 38.12 1.10 0.65 0.86 1.56 1.94 2.04
C17orf104 ENST00000409122 29.22 0.69 12.50 1.10 4.10 2.21 1.56 0.28 0.50
ZNF322 ENST00000415922 29.22 27.81 26.68 1.10 1.23 1.00 1.56 1.19 1.26
FAM102B ENST00000370035 29.23 40.71 33.13 1.10 0.63 0.87 1.56 1.78 1.69
RPIA ENST00000283646 29.23 45.72 35.61 1.10 0.75 0.86 1.57 2.02 1.76
TGFBR3 ENST00000212355 29.24 24.50 24.92 1.10 1.32 1.02 1.56 1.01 1.11
MAP1S ENST00000324096 29.24 21.73 23.60 1.10 1.46 1.19 1.57 0.81 1.02
KDM1B ENST00000297792 29.25 27.67 26.59 1.09 1.27 0.97 1.57 1.19 1.25
RAD51L3-RFFL ENST00000593039 29.25 60.71 43.37 1.09 0.54 0.63 1.57 1.39 2.01
RGS7BP ENST00000334025 29.26 14.23 19.78 1.09 2.06 1.49 1.57 0.61 0.85
SLC35D3 ENST00000331858 29.27 51.83 38.85 1.09 0.61 0.81 1.58 1.87 2.05
MTPAP ENST00000263063 29.27 5.20 15.05 1.09 3.18 1.87 1.58 0.32 0.63
SLC43A1 ENST00000278426 29.28 40.07 32.84 1.09 0.63 0.85 1.57 1.70 1.65
CASC4 ENST00000299957 29.28 36.39 31.05 1.09 0.82 0.84 1.57 1.63 1.51
ZFP3 ENST00000318833 29.29 47.07 36.30 1.09 0.67 0.85 1.57 1.99 1.86
FNBP4 ENST00000263773 29.29 2.86 13.72 1.09 3.51 2.05 1.57 0.28 0.58
EXOC6B ENST00000272427 29.30 18.46 21.99 1.09 1.48 1.19 1.57 0.76 0.97
KIFC3 ENST00000379655 29.30 23.32 24.36 1.09 1.43 1.08 1.57 0.93 1.07
ARHGAP21 ENST00000396432 29.31 3.77 14.24 1.09 3.32 2.00 1.57 0.31 0.60
MYT1 ENST00000328439 29.31 12.96 19.13 1.10 2.06 1.53 1.56 0.59 0.85

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