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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
LYZL6 ENST00000585556 55.14 85.52 73.08 0.62 0.27 0.42 1.70 0.44 0.80
ALG2 ENST00000476832 55.15 65.92 61.14 0.62 0.54 0.43 1.70 1.24 1.51
GTDC1 ENST00000392869 55.15 70.77 64.24 0.62 0.48 0.51 1.69 1.08 1.35
TMCO5A ENST00000319669 55.16 56.28 55.36 0.62 0.52 0.49 1.69 1.55 1.73
CUTA ENST00000374500 55.16 85.25 72.96 0.62 0.25 0.40 1.68 0.46 0.81
ITIH2 ENST00000358415 55.17 58.41 56.60 0.62 0.54 0.52 1.69 1.40 1.71
GXYLT2 ENST00000389617 55.17 82.18 71.14 0.62 0.34 0.43 1.69 0.52 0.87
FN3KRP ENST00000269373 55.18 80.95 70.37 0.61 0.35 0.43 1.69 0.57 0.91
DEPTOR ENST00000286234 55.18 76.31 67.55 0.61 0.43 0.51 1.69 0.86 1.12
COL24A1 ENST00000370571 55.19 49.56 51.52 0.61 0.66 0.62 1.69 2.02 1.92
ADAM21 ENST00000603540 55.19 78.31 68.77 0.61 0.43 0.46 1.69 0.74 1.05
RBKS ENST00000302188 55.20 78.16 68.69 0.61 0.43 0.47 1.69 0.73 1.05
PNPLA2 ENST00000336615 55.20 40.11 46.36 0.61 0.63 0.67 1.69 1.71 1.89
CCR1 ENST00000296140 55.21 38.60 45.63 0.61 0.73 0.68 1.69 1.66 1.98
ACP1 ENST00000272067 55.21 89.59 75.31 0.61 0.27 0.37 1.68 0.37 0.65
MRPS10 ENST00000053468 55.22 84.23 72.42 0.61 0.27 0.44 1.69 0.44 0.83
PSMG1 ENST00000331573 55.22 47.87 50.57 0.61 0.59 0.67 1.69 1.97 1.86
COX4I1 ENST00000562336 55.23 36.75 44.52 0.61 0.76 0.62 1.69 1.66 2.04
HDDC2 ENST00000398153 55.23 66.45 61.55 0.61 0.56 0.46 1.69 1.20 1.48
FBP2 ENST00000375337 55.24 54.10 54.18 0.61 0.65 0.61 1.69 1.68 1.73
MMAB ENST00000545712 55.25 47.27 50.27 0.61 0.66 0.65 1.69 2.01 1.92
RAD52 ENST00000358495 55.25 60.76 58.07 0.61 0.56 0.47 1.68 1.39 1.66
GIP ENST00000357424 55.26 42.68 47.83 0.61 0.61 0.65 1.68 1.91 1.89
KIAA0101 ENST00000300035 55.26 54.75 54.58 0.61 0.58 0.56 1.68 1.63 1.73
TYW1 ENST00000359626 55.27 40.02 46.31 0.61 0.63 0.67 1.68 1.68 1.91

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