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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
FAM160B1 ENST00000369248 25.70 9.36 15.29 1.35 2.48 1.82 1.20 0.49 0.66
WDR43 ENST00000407426 25.71 1.95 11.50 1.35 3.75 2.19 1.20 0.25 0.45
LAMP1 ENST00000332556 25.71 18.65 20.24 1.34 1.49 1.48 1.20 0.75 0.88
PCDHAC2 ENST00000289269 25.72 15.22 18.42 1.34 1.90 1.62 1.20 0.67 0.81
SLC13A4 ENST00000354042 25.72 16.77 19.22 1.34 1.68 1.54 1.20 0.71 0.85
PGGT1B ENST00000419445 25.73 28.73 25.32 1.34 1.15 1.05 1.20 1.29 1.16
DRD3 ENST00000383673 25.73 44.59 33.34 1.34 0.65 0.87 1.20 1.97 1.71
MFSD4 ENST00000367147 25.74 36.84 29.46 1.34 0.76 0.85 1.20 1.66 1.37
WIPI1 ENST00000262139 25.74 36.75 29.42 1.34 0.76 0.84 1.20 1.65 1.36
RBMS2 ENST00000262031 25.75 43.32 32.74 1.34 0.61 0.86 1.20 1.94 1.65
FASLG ENST00000367721 25.75 37.99 30.04 1.34 0.77 0.81 1.20 1.71 1.46
WAS ENST00000376701 25.76 3.15 12.03 1.34 3.46 2.30 1.20 0.28 0.47
METTL21B ENST00000300209 25.76 81.98 53.29 1.34 0.35 0.61 1.20 0.50 1.86
MTR ENST00000366577 25.77 29.81 25.94 1.34 1.13 1.00 1.20 1.40 1.24
CSMD3 ENST00000297405 25.77 11.25 16.32 1.34 2.13 1.71 1.20 0.55 0.67
TCEB3 ENST00000418390 25.78 1.90 11.51 1.34 3.74 2.19 1.20 0.26 0.45
CCNE1 ENST00000262643 25.78 14.29 17.94 1.34 2.06 1.70 1.20 0.61 0.77
TBC1D14 ENST00000409757 25.79 22.83 22.50 1.34 1.44 1.16 1.20 0.89 0.97
LCT ENST00000264162 25.79 16.22 19.00 1.34 1.80 1.54 1.20 0.69 0.85
SLC7A3 ENST00000374299 25.80 5.79 13.40 1.34 2.86 2.05 1.20 0.34 0.55
PPM1K ENST00000608933 25.80 56.94 39.73 1.34 0.56 0.78 1.21 1.53 2.02
BTBD11 ENST00000280758 25.81 6.12 13.61 1.34 2.75 2.01 1.21 0.35 0.57
SLA ENST00000427060 25.81 27.45 24.69 1.34 1.25 1.05 1.21 1.17 1.10
PRRC2C ENST00000338920 25.82 1.50 11.36 1.34 3.89 2.20 1.21 0.26 0.45
SDCBP ENST00000260130 25.83 59.52 40.87 1.34 0.51 0.80 1.21 1.41 2.06

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