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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
MSANTD2 ENST00000239614 15.11 16.70 13.52 1.57 1.70 2.05 0.74 0.71 0.57
TFAP2D ENST00000008391 15.12 8.78 9.40 1.57 2.47 2.29 0.74 0.48 0.39
CHMP7 ENST00000397677 15.12 17.22 13.81 1.57 1.61 2.09 0.75 0.74 0.57
DDX41 ENST00000507955 15.13 38.09 24.66 1.57 0.77 1.06 0.75 1.70 1.10
PTPRT ENST00000373187 15.13 3.72 6.77 1.57 3.34 2.99 0.75 0.30 0.32
TRHDE ENST00000261180 15.14 24.52 17.72 1.57 1.30 1.66 0.75 1.03 0.78
ARHGEF7 ENST00000375741 15.14 5.09 7.48 1.57 3.20 2.78 0.75 0.33 0.33
TTBK1 ENST00000259750 15.15 6.38 8.12 1.57 2.66 2.58 0.76 0.37 0.37
IHH ENST00000295731 15.15 31.14 21.23 1.57 1.01 1.40 0.76 1.36 0.90
TNFSF11 ENST00000239849 15.16 44.71 28.12 1.57 0.66 0.81 0.76 1.98 1.28
ATP8A1 ENST00000381668 15.16 15.74 13.05 1.57 1.87 2.09 0.76 0.69 0.52
GREB1L ENST00000580732 15.17 0.20 4.97 1.56 4.14 3.70 0.76 0.28 0.25
CWC27 ENST00000381070 15.17 47.92 29.71 1.57 0.59 0.86 0.76 1.99 1.41
IBTK ENST00000306270 15.18 19.83 15.27 1.57 1.42 1.83 0.76 0.74 0.66
CCNE2 ENST00000520509 15.19 17.20 13.89 1.57 1.59 2.10 0.76 0.75 0.59
ACSL4 ENST00000340800 15.19 12.11 11.34 1.57 2.06 2.20 0.76 0.57 0.45
MOB1A ENST00000396049 15.20 13.26 11.84 1.57 2.05 2.23 0.75 0.60 0.45
ATP1B3 ENST00000286371 15.20 35.87 23.64 1.57 0.80 1.19 0.75 1.58 1.01
PPARGC1A ENST00000264867 15.21 5.64 7.76 1.57 2.97 2.64 0.75 0.33 0.33
SKIDA1 ENST00000449193 15.21 8.95 9.54 1.57 2.44 2.30 0.75 0.47 0.40
EFEMP1 ENST00000394555 15.22 3.06 6.47 1.57 3.47 3.06 0.75 0.28 0.32
AGAP2 ENST00000547588 15.22 8.85 9.49 1.57 2.45 2.30 0.75 0.48 0.40
RNF38 ENST00000259605 15.23 2.75 6.28 1.57 3.53 3.14 0.75 0.28 0.32
SEPT3 ENST00000396426 15.23 26.85 19.04 1.57 1.23 1.54 0.75 1.12 0.85
XKR6 ENST00000416569 15.24 6.12 8.05 1.57 2.76 2.58 0.75 0.35 0.37

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