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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
CCDC8 ENST00000307522 85.72 46.08 67.79 0.27 0.76 0.51 0.46 2.03 1.12
CD3E ENST00000361763 87.18 48.84 70.27 0.23 0.63 0.43 0.38 2.03 0.91
PRR26 ENST00000441152 98.35 45.97 75.08 0.10 0.76 0.39 0.10 2.03 0.67
CD46 ENST00000322875 99.88 48.85 77.58 0.12 0.63 0.37 0.14 2.03 0.56
LIN7C ENST00000278193 6.45 46.22 24.39 3.05 0.73 1.08 0.37 2.04 1.07
TXN ENST00000374517 7.47 49.13 26.38 2.77 0.66 1.01 0.39 2.04 1.25
UBE2G2 ENST00000345496 8.64 46.06 25.42 2.43 0.76 1.04 0.44 2.04 1.17
POLR2D ENST00000272645 9.61 49.12 27.50 2.15 0.66 0.97 0.48 2.04 1.27
KCNJ13 ENST00000233826 9.80 49.08 27.58 2.11 0.67 0.96 0.50 2.04 1.26
CDK2AP1 ENST00000261692 12.56 46.25 27.52 1.67 0.73 0.96 0.63 2.04 1.27
TMEM117 ENST00000266534 14.72 46.31 28.67 1.56 0.73 0.80 0.74 2.04 1.34
KLF10 ENST00000285407 14.75 46.16 28.61 1.57 0.73 0.80 0.74 2.04 1.35
VDR ENST00000550325 18.91 46.22 30.84 1.57 0.73 0.78 0.94 2.04 1.49
ATF3 ENST00000341491 21.17 46.39 32.01 1.53 0.73 0.90 1.03 2.04 1.59
BRCC3 ENST00000369462 21.35 48.92 33.29 1.54 0.63 0.89 1.07 2.04 1.70
DBP ENST00000222122 22.60 46.17 32.60 1.46 0.73 0.87 1.05 2.04 1.63
ZKSCAN8 ENST00000330236 28.03 46.40 35.42 1.16 0.73 0.87 1.48 2.04 1.77
SMYD2 ENST00000366957 29.76 46.33 36.14 1.06 0.73 0.87 1.58 2.04 1.80
SOAT1 ENST00000367619 32.52 49.12 39.20 0.96 0.66 0.78 1.70 2.04 2.06
CPXM1 ENST00000380605 32.60 49.21 39.29 0.96 0.66 0.80 1.70 2.04 2.04
COMMD1 ENST00000311832 34.59 49.19 40.18 0.99 0.66 0.82 1.79 2.04 1.99
RPP40 ENST00000380051 36.47 49.54 41.21 0.95 0.66 0.76 1.80 2.04 2.02
ATG7 ENST00000354449 38.87 48.92 42.13 0.91 0.65 0.71 1.74 2.04 2.00
MANEAL ENST00000373045 39.44 46.05 40.95 0.90 0.77 0.77 1.78 2.04 2.06
SESN2 ENST00000253063 42.42 49.09 44.20 0.76 0.66 0.62 1.75 2.04 2.05

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