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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
AXIN2 ENST00000307078 39.90 17.83 27.04 0.89 1.52 0.99 1.75 0.72 1.29
BCORL1 ENST00000540052 39.91 3.50 19.74 0.89 3.38 1.52 1.75 0.29 0.85
FOXN1 ENST00000226247 39.92 15.90 26.09 0.87 1.89 0.99 1.76 0.68 1.25
SAMD9L ENST00000318238 39.92 42.12 39.38 0.87 0.61 0.78 1.76 1.86 2.04
FASTKD5 ENST00000380266 39.93 50.71 43.66 0.87 0.63 0.59 1.76 1.95 2.02
N4BP2 ENST00000261435 39.93 30.63 33.44 0.87 1.06 0.89 1.75 1.38 1.70
XPNPEP3 ENST00000357137 39.94 47.87 42.13 0.87 0.59 0.71 1.75 1.97 2.00
PCDHB1 ENST00000306549 39.94 70.25 54.69 0.87 0.52 0.56 1.75 1.12 1.73
SST ENST00000287641 39.95 56.97 47.22 0.87 0.56 0.67 1.75 1.53 1.89
KIAA1737 ENST00000361786 39.95 41.28 38.94 0.87 0.61 0.80 1.75 1.82 2.06
PLEKHO1 ENST00000369124 39.96 23.29 29.83 0.87 1.43 0.86 1.75 0.93 1.43
LHFPL1 ENST00000371968 39.96 60.13 48.93 0.87 0.52 0.71 1.75 1.39 1.84
SLC8A3 ENST00000381269 39.97 30.22 33.24 0.87 1.09 0.87 1.75 1.41 1.69
PTGS1 ENST00000362012 39.97 40.26 38.41 0.86 0.61 0.84 1.76 1.73 2.04
MEA1 ENST00000244711 39.98 83.67 62.78 0.86 0.27 0.48 1.75 0.47 1.39
NDUFAF6 ENST00000396124 39.98 66.33 52.45 0.86 0.54 0.61 1.76 1.20 1.92
PRCD ENST00000586148 39.99 82.79 62.21 0.86 0.32 0.48 1.76 0.50 1.44
SLC22A15 ENST00000369503 39.99 49.80 43.25 0.86 0.66 0.65 1.76 2.02 1.99
LRRC23 ENST00000007969 40.00 68.09 53.46 0.86 0.52 0.62 1.76 1.20 1.83
SGCA ENST00000262018 40.00 43.36 40.03 0.86 0.59 0.82 1.76 1.94 1.99
ASF1B ENST00000263382 40.01 81.15 61.26 0.86 0.35 0.43 1.76 0.55 1.48
CMC4 ENST00000369484 40.01 70.29 54.74 0.86 0.52 0.56 1.75 1.10 1.73
S1PR2 ENST00000590320 40.02 59.09 48.45 0.86 0.49 0.68 1.75 1.43 1.87
LIPT1 ENST00000393477 40.02 86.41 64.56 0.86 0.25 0.51 1.75 0.42 1.33
HSPA14 ENST00000378372 40.03 19.38 27.85 0.86 1.47 0.87 1.75 0.74 1.28

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