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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
SLC22A2 ENST00000366953 61.86 64.29 64.34 0.70 0.49 0.51 1.29 1.20 1.35
KRTAP3-3 ENST00000391586 61.86 96.11 82.37 0.70 0.21 0.33 1.29 0.20 0.44
MEIG1 ENST00000407572 61.87 88.11 78.26 0.70 0.24 0.37 1.30 0.38 0.55
MAFK ENST00000343242 61.87 37.64 48.64 0.70 0.78 0.67 1.29 1.71 1.85
RNF183 ENST00000478815 61.88 90.33 79.39 0.71 0.25 0.39 1.29 0.38 0.52
C1orf194 ENST00000369949 61.88 87.34 77.80 0.71 0.22 0.38 1.29 0.41 0.54
FAM81B ENST00000283357 61.89 66.63 65.87 0.71 0.54 0.51 1.29 1.22 1.24
OR52N2 ENST00000317037 61.89 94.33 81.45 0.71 0.24 0.35 1.29 0.24 0.48
NCKAP5 ENST00000409261 61.90 22.25 40.34 0.71 1.53 0.80 1.30 0.81 2.01
ABCA9 ENST00000340001 61.90 57.01 59.84 0.71 0.56 0.49 1.30 1.51 1.63
UQCRH ENST00000311672 61.91 72.01 69.04 0.71 0.51 0.46 1.30 1.04 1.03
IRS4 ENST00000372129 61.91 20.07 39.36 0.71 1.44 0.78 1.31 0.74 2.04
SLC5A4 ENST00000266086 61.92 62.57 63.40 0.71 0.52 0.49 1.30 1.31 1.37
DLK1 ENST00000341267 61.92 37.05 48.34 0.71 0.77 0.67 1.30 1.68 1.88
FSCN2 ENST00000334850 61.93 77.94 72.61 0.71 0.42 0.46 1.29 0.79 0.81
SMPDL3B ENST00000373894 61.93 72.57 69.40 0.71 0.47 0.43 1.29 1.04 0.98
RBAK ENST00000396912 61.94 49.97 55.64 0.71 0.66 0.53 1.29 2.02 1.73
CEP152 ENST00000380950 61.94 44.07 52.27 0.71 0.61 0.59 1.29 1.98 1.90
TSPAN1 ENST00000372003 61.95 75.33 71.07 0.71 0.49 0.43 1.29 0.90 0.86
TNFAIP2 ENST00000560869 61.95 35.60 47.54 0.71 0.78 0.65 1.29 1.58 1.89
ASCL3 ENST00000325884 61.96 84.11 76.05 0.71 0.27 0.38 1.29 0.45 0.62
NIPSNAP3B ENST00000374762 61.96 83.38 75.66 0.71 0.27 0.38 1.29 0.47 0.64
PWP2 ENST00000291576 61.97 26.00 42.22 0.71 1.20 0.68 1.29 1.10 2.01
SEC14L5 ENST00000251170 61.98 67.26 66.31 0.71 0.56 0.53 1.29 1.22 1.21
GUCA1C ENST00000261047 61.98 92.75 80.67 0.71 0.29 0.39 1.29 0.30 0.52

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