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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
ABCA6 ENST00000284425 79.42 45.59 63.74 0.34 0.75 0.49 0.58 1.99 1.38
PIK3C2G ENST00000433979 79.42 60.38 72.58 0.34 0.53 0.46 0.58 1.41 0.82
BPIFA1 ENST00000354297 79.43 85.37 85.71 0.34 0.25 0.33 0.59 0.45 0.33
CLIC3 ENST00000494426 79.43 91.20 88.45 0.34 0.23 0.22 0.59 0.35 0.29
SRFBP1 ENST00000339397 79.44 72.60 79.33 0.34 0.47 0.39 0.59 1.04 0.53
ARHGEF38 ENST00000420470 79.44 49.43 66.11 0.34 0.65 0.51 0.59 2.01 1.20
NTSR2 ENST00000306928 79.45 61.65 73.33 0.34 0.54 0.43 0.58 1.39 0.78
C14orf159 ENST00000518868 79.45 82.13 84.06 0.34 0.34 0.35 0.58 0.51 0.42
OR5B17 ENST00000357377 79.46 81.98 84.00 0.34 0.35 0.35 0.57 0.50 0.42
MALSU1 ENST00000466681 79.46 95.02 90.28 0.34 0.23 0.15 0.58 0.21 0.22
ZBTB45 ENST00000594051 79.47 61.40 73.17 0.34 0.54 0.43 0.58 1.40 0.79
SLC10A1 ENST00000216540 79.47 97.39 91.34 0.34 0.22 0.15 0.58 0.19 0.18
RGSL1 ENST00000294854 79.48 36.80 58.23 0.34 0.75 0.48 0.58 1.66 1.64
HAP1 ENST00000347901 79.48 85.01 85.61 0.34 0.25 0.32 0.58 0.45 0.35
EMR3 ENST00000253673 79.49 76.17 81.16 0.34 0.43 0.39 0.57 0.86 0.49
CSNK1A1L ENST00000379800 79.49 67.17 76.43 0.34 0.54 0.38 0.57 1.22 0.62
CCL18 ENST00000004921 79.50 89.41 87.59 0.34 0.27 0.27 0.57 0.37 0.31
JMJD8 ENST00000412368 79.51 88.73 87.31 0.34 0.25 0.28 0.57 0.35 0.31
REXO1 ENST00000170168 79.51 12.69 44.66 0.34 2.10 0.62 0.57 0.58 2.06
ZNF273 ENST00000476120 79.52 72.26 79.21 0.34 0.51 0.38 0.57 1.03 0.54
ANKRD26 ENST00000376087 79.52 38.25 59.04 0.34 0.76 0.49 0.57 1.70 1.66
BASP1 ENST00000322611 79.53 42.98 61.98 0.34 0.62 0.49 0.57 1.89 1.46
ASRGL1 ENST00000415229 79.53 75.06 80.62 0.34 0.51 0.39 0.57 0.91 0.51
SWSAP1 ENST00000312423 79.54 82.10 84.09 0.34 0.34 0.35 0.57 0.50 0.42
FAHD2B ENST00000414820 79.54 69.17 77.57 0.34 0.56 0.37 0.57 1.12 0.57

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