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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
KRTAP1-1 ENST00000306271 77.61 93.76 88.78 0.34 0.27 0.19 0.67 0.26 0.28
EPSTI1 ENST00000313640 77.61 85.83 85.08 0.34 0.28 0.33 0.67 0.43 0.38
ARRDC2 ENST00000222250 77.62 69.26 76.53 0.34 0.57 0.38 0.67 1.14 0.61
C2orf70 ENST00000329615 77.63 81.82 83.09 0.34 0.35 0.30 0.67 0.51 0.40
HILPDA ENST00000257696 77.63 91.89 87.88 0.34 0.23 0.24 0.67 0.32 0.32
FAM83E ENST00000263266 77.64 82.92 83.68 0.34 0.32 0.33 0.67 0.49 0.40
SLC25A18 ENST00000327451 77.64 70.40 77.19 0.34 0.52 0.35 0.67 1.08 0.59
TTC31 ENST00000233623 77.65 70.67 77.33 0.34 0.49 0.35 0.67 1.09 0.58
FBXW5 ENST00000325285 77.65 80.83 82.66 0.34 0.35 0.32 0.67 0.57 0.43
PDLIM2 ENST00000308354 77.66 46.96 63.50 0.34 0.71 0.49 0.67 1.95 1.39
CCDC180 ENST00000375202 77.66 50.51 65.70 0.34 0.63 0.51 0.67 1.95 1.27
LTK ENST00000263800 77.67 66.74 75.14 0.34 0.56 0.38 0.67 1.21 0.67
MMP17 ENST00000360564 77.67 57.79 69.94 0.34 0.57 0.47 0.67 1.47 0.92
SLC2A6 ENST00000371899 77.68 50.82 65.86 0.34 0.63 0.51 0.67 1.93 1.25
LAPTM5 ENST00000294507 77.68 18.57 46.86 0.34 1.49 0.68 0.67 0.76 1.88
FUT1 ENST00000310160 77.69 73.82 79.07 0.34 0.53 0.39 0.67 1.02 0.53
LANCL3 ENST00000378619 77.69 37.93 57.82 0.34 0.78 0.51 0.67 1.70 1.66
PCM1 ENST00000325083 77.70 27.62 51.82 0.34 1.28 0.62 0.67 1.17 1.92
MIB2 ENST00000505820 77.70 30.60 53.58 0.34 1.08 0.63 0.67 1.39 1.80
KCNG4 ENST00000308251 77.71 94.54 89.25 0.34 0.23 0.19 0.67 0.24 0.25
VOPP1 ENST00000285279 77.71 40.42 59.29 0.34 0.61 0.51 0.67 1.76 1.68
NACA2 ENST00000521764 77.72 92.57 88.32 0.34 0.29 0.22 0.67 0.31 0.30
PTPRN2 ENST00000389418 77.72 26.81 51.37 0.34 1.23 0.63 0.67 1.12 1.90
KRTAP4-5 ENST00000343246 77.73 85.49 84.95 0.34 0.27 0.33 0.67 0.45 0.40
MR1 ENST00000367580 77.73 92.07 88.06 0.34 0.24 0.23 0.67 0.32 0.31

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