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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
MAT2B ENST00000321757 12.40 34.96 21.81 1.66 0.76 1.23 0.62 1.55 0.94
MSI1 ENST00000257552 12.41 9.77 8.46 1.66 2.42 2.52 0.62 0.50 0.37
AP1B1 ENST00000357586 12.41 10.17 8.63 1.66 2.30 2.53 0.63 0.49 0.36
ABCC5 ENST00000334444 12.42 17.15 12.38 1.64 1.61 2.23 0.63 0.75 0.50
ZMIZ1 ENST00000334512 12.42 9.44 8.28 1.64 2.48 2.57 0.63 0.49 0.37
POLR3E ENST00000299853 12.43 22.29 15.13 1.64 1.53 1.86 0.63 0.83 0.64
C2CD5 ENST00000333957 12.43 36.03 22.40 1.64 0.80 1.15 0.64 1.58 0.96
CLASP2 ENST00000468888 12.44 5.17 6.07 1.64 3.20 3.28 0.64 0.32 0.30
NPAS4 ENST00000311034 12.44 14.04 10.85 1.64 2.07 2.19 0.64 0.59 0.44
RP11-73M18.2 ENST00000472726 12.45 25.15 16.67 1.64 1.32 1.70 0.64 1.03 0.70
TIA1 ENST00000433529 12.45 21.94 15.01 1.66 1.47 1.89 0.64 0.80 0.63
UBE4B ENST00000343090 12.46 3.44 5.21 1.67 3.40 3.56 0.64 0.29 0.26
ARPC5 ENST00000294742 12.46 30.57 19.51 1.67 1.08 1.54 0.64 1.39 0.83
VSTM2A ENST00000407838 12.47 32.28 20.47 1.67 0.86 1.49 0.64 1.46 0.89
IWS1 ENST00000295321 12.47 9.84 8.52 1.66 2.39 2.51 0.64 0.50 0.37
STK32C ENST00000298630 12.48 24.12 16.11 1.66 1.35 1.71 0.64 0.98 0.66
BTRC ENST00000370187 12.48 22.34 15.18 1.66 1.51 1.83 0.64 0.82 0.64
ANKS1B ENST00000547776 12.49 5.91 6.54 1.66 2.82 3.02 0.64 0.35 0.32
SAMD8 ENST00000542569 12.49 38.16 23.43 1.67 0.77 1.19 0.64 1.72 1.02
NFKBIE ENST00000275015 12.50 20.67 14.29 1.67 1.47 2.01 0.64 0.78 0.60
EFNB3 ENST00000226091 12.50 34.68 21.72 1.67 0.80 1.25 0.64 1.55 0.93
NCOA5 ENST00000290231 12.51 6.56 6.90 1.67 2.63 2.90 0.64 0.37 0.33
SLC25A11 ENST00000225665 12.51 28.25 18.29 1.67 1.18 1.66 0.64 1.22 0.79
LATS1 ENST00000543571 12.52 7.57 7.42 1.67 2.51 2.80 0.64 0.42 0.34
HOXA11 ENST00000006015 12.53 14.20 11.01 1.67 2.06 2.20 0.63 0.60 0.44

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