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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
FAM229B ENST00000368656 37.45 60.91 48.05 0.92 0.56 0.67 1.75 1.40 1.88
ALDH1L2 ENST00000258494 37.46 50.33 42.14 0.92 0.66 0.71 1.75 1.96 2.00
CALR ENST00000316448 37.46 17.43 25.55 0.92 1.59 1.05 1.75 0.74 1.19
FDPS ENST00000356657 37.47 34.87 34.42 0.92 0.76 0.90 1.75 1.55 1.76
VPS53 ENST00000437048 37.47 32.64 33.22 0.92 0.85 0.87 1.75 1.46 1.68
KIAA1191 ENST00000298569 37.48 59.27 47.11 0.92 0.49 0.68 1.75 1.42 1.89
NDUFA8 ENST00000373768 37.48 37.43 35.59 0.92 0.75 0.86 1.75 1.66 1.77
LRRC55 ENST00000497933 37.49 47.56 40.67 0.92 0.61 0.81 1.75 2.02 2.04
PPP4R4 ENST00000304338 37.49 31.17 32.52 0.92 1.01 0.89 1.76 1.36 1.61
SLC25A37 ENST00000519973 37.50 30.03 31.97 0.92 1.09 0.90 1.77 1.43 1.58
GPX5 ENST00000412168 37.50 68.27 52.12 0.92 0.52 0.61 1.77 1.20 1.92
NME5 ENST00000265191 37.51 69.51 52.81 0.94 0.54 0.61 1.77 1.12 1.88
CABP7 ENST00000216144 37.51 40.27 37.13 0.94 0.61 0.81 1.77 1.74 1.96
ATP11B ENST00000323116 37.52 18.43 26.15 0.94 1.48 0.99 1.77 0.75 1.27
KHDRBS2 ENST00000281156 37.52 32.33 33.07 0.94 0.86 0.87 1.77 1.46 1.66
ZNF382 ENST00000292928 37.53 32.47 33.16 0.94 0.86 0.87 1.77 1.48 1.69
NLE1 ENST00000442241 37.53 32.65 33.24 0.94 0.85 0.87 1.77 1.46 1.69
ESYT1 ENST00000541590 37.54 33.68 33.78 0.94 0.84 0.89 1.77 1.56 1.74
SEMA7A ENST00000261918 37.54 22.49 28.22 0.94 1.51 0.81 1.77 0.84 1.29
UBE2D4 ENST00000222402 37.55 77.33 57.37 0.94 0.42 0.51 1.77 0.77 1.67
ZNRF2 ENST00000323037 37.55 53.57 43.96 0.94 0.63 0.61 1.76 1.70 2.02
CASP3 ENST00000308394 37.56 32.76 33.33 0.92 0.84 0.89 1.76 1.44 1.71
AMOTL2 ENST00000249883 37.57 21.26 27.54 0.92 1.42 0.96 1.76 0.81 1.27
NGDN ENST00000408901 37.57 58.80 46.92 0.92 0.54 0.70 1.76 1.41 1.87
MTMR6 ENST00000381801 37.58 40.31 37.22 0.92 0.62 0.81 1.76 1.74 1.98

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