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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
BEST3 ENST00000330891 52.95 74.42 65.13 0.65 0.53 0.51 1.77 1.00 1.31
TMPRSS11A ENST00000334830 52.95 70.17 62.41 0.65 0.53 0.48 1.77 1.12 1.40
C15orf27 ENST00000388942 52.96 56.59 54.32 0.65 0.53 0.59 1.77 1.55 1.74
DRGX ENST00000434016 52.96 66.62 60.24 0.65 0.54 0.47 1.77 1.22 1.60
SIRT2 ENST00000249396 52.97 53.84 52.72 0.65 0.63 0.61 1.77 1.71 1.88
AMBN ENST00000322937 52.97 60.48 56.54 0.65 0.52 0.52 1.77 1.41 1.70
EVA1C ENST00000300255 52.98 40.51 45.44 0.63 0.63 0.70 1.77 1.77 1.99
KDELC1 ENST00000376004 52.98 54.84 53.32 0.63 0.57 0.62 1.77 1.63 1.86
WDR6 ENST00000395474 52.99 41.70 46.06 0.63 0.61 0.68 1.77 1.80 1.97
DENR ENST00000280557 52.99 22.81 36.02 0.63 1.46 0.87 1.77 0.88 1.79
GPATCH3 ENST00000361720 53.00 68.13 61.23 0.63 0.53 0.43 1.77 1.21 1.49
BRMS1 ENST00000425825 53.00 62.96 58.03 0.63 0.51 0.47 1.77 1.31 1.66
PLTP ENST00000477313 53.01 56.70 54.40 0.63 0.53 0.58 1.77 1.56 1.75
HORMAD2 ENST00000336726 53.01 49.92 50.48 0.63 0.66 0.67 1.76 2.02 1.87
RASSF3 ENST00000542104 53.02 79.60 68.29 0.63 0.38 0.51 1.76 0.66 1.08
RTEL1 ENST00000508582 53.02 25.90 37.69 0.63 1.21 0.84 1.76 1.08 2.01
EEFSEC ENST00000254730 53.03 66.70 60.33 0.63 0.56 0.46 1.76 1.22 1.58
FCHSD1 ENST00000435817 53.03 69.90 62.29 0.63 0.53 0.49 1.76 1.15 1.43
BPIFB4 ENST00000375483 53.04 73.52 64.62 0.63 0.53 0.51 1.76 1.03 1.32
TMEM51 ENST00000428417 53.04 40.33 45.40 0.63 0.61 0.70 1.76 1.74 2.01
BNIP1 ENST00000231668 53.05 65.76 59.72 0.63 0.54 0.49 1.76 1.22 1.66
P2RX4 ENST00000359949 53.06 70.12 62.43 0.63 0.53 0.48 1.77 1.12 1.39
LRRC8E ENST00000306708 53.06 48.73 49.88 0.63 0.63 0.63 1.77 1.99 1.89
SMIM15 ENST00000339020 53.07 86.05 72.21 0.63 0.27 0.43 1.78 0.43 0.82
SERGEF ENST00000265965 53.07 68.70 61.61 0.63 0.53 0.46 1.78 1.17 1.48

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