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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
MBOAT7 ENST00000245615 53.33 30.32 40.12 0.62 1.06 0.81 1.75 1.41 1.99
BEST1 ENST00000449131 53.34 78.98 68.14 0.62 0.40 0.49 1.75 0.69 1.08
WWC2 ENST00000403733 53.34 28.51 39.31 0.62 1.15 0.80 1.75 1.25 2.04
PPID ENST00000307720 53.35 64.68 59.22 0.62 0.48 0.49 1.76 1.24 1.68
SUCNR1 ENST00000362032 53.35 67.49 61.03 0.62 0.54 0.43 1.76 1.20 1.55
SUCLG2 ENST00000493112 53.36 81.39 69.55 0.62 0.33 0.44 1.76 0.54 0.96
POPDC2 ENST00000264231 53.37 57.34 54.91 0.62 0.54 0.51 1.76 1.49 1.74
CENPP ENST00000375587 53.37 35.23 42.55 0.62 0.76 0.68 1.76 1.58 2.01
RPUSD2 ENST00000315616 53.38 58.02 55.34 0.62 0.53 0.49 1.77 1.45 1.73
GCDH ENST00000222214 53.38 34.39 42.10 0.62 0.84 0.71 1.77 1.56 1.99
MFSD8 ENST00000296468 53.39 59.19 55.97 0.62 0.49 0.49 1.77 1.44 1.76
EPB42 ENST00000300215 53.39 41.16 46.00 0.62 0.59 0.68 1.77 1.82 1.97
ARMC4 ENST00000305242 53.40 64.11 58.87 0.62 0.49 0.49 1.77 1.20 1.65
ACY1 ENST00000404366 53.40 60.99 57.08 0.62 0.54 0.52 1.76 1.41 1.71
CDHR3 ENST00000317716 53.41 70.62 63.09 0.62 0.51 0.49 1.76 1.08 1.39
TSTD2 ENST00000341170 53.41 67.06 60.82 0.62 0.54 0.43 1.75 1.23 1.60
NSMCE1 ENST00000361439 53.42 60.47 56.74 0.62 0.52 0.53 1.75 1.41 1.70
ZFP1 ENST00000393430 53.42 36.80 43.50 0.62 0.75 0.62 1.75 1.66 2.00
MAK ENST00000313243 53.43 65.10 59.58 0.62 0.51 0.49 1.75 1.24 1.69
ESYT2 ENST00000251527 53.43 28.50 39.35 0.62 1.16 0.78 1.75 1.25 2.04
ENO3 ENST00000323997 53.44 87.75 73.38 0.62 0.24 0.42 1.75 0.37 0.78
IL4R ENST00000395762 53.44 45.09 48.14 0.62 0.68 0.66 1.75 1.97 1.87
IER3 ENST00000259874 53.45 51.10 51.39 0.62 0.66 0.63 1.75 1.92 1.90
LYRM4 ENST00000500576 53.45 80.58 69.09 0.62 0.37 0.44 1.75 0.57 1.00
LIF ENST00000249075 53.46 42.18 46.47 0.62 0.61 0.67 1.75 1.87 1.91

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