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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
OR13C2 ENST00000542196 85.62 85.20 88.52 0.28 0.25 0.22 0.46 0.45 0.28
ADIRF ENST00000372013 85.62 89.36 90.56 0.28 0.27 0.15 0.46 0.37 0.21
FAM122C ENST00000370784 85.63 77.97 85.16 0.28 0.42 0.33 0.46 0.79 0.37
HSD17B2 ENST00000199936 85.63 86.22 89.04 0.28 0.27 0.19 0.46 0.42 0.26
UGT2B11 ENST00000446444 85.64 83.44 87.70 0.28 0.27 0.24 0.46 0.47 0.31
KRTAP19-5 ENST00000334151 85.64 99.65 95.43 0.28 0.17 0.08 0.46 0.12 0.11
MEIOB ENST00000412554 85.65 76.90 84.62 0.27 0.43 0.34 0.46 0.79 0.40
GGN ENST00000334928 85.65 46.79 68.21 0.27 0.72 0.51 0.46 1.97 1.08
SLC38A10 ENST00000374759 85.66 46.70 68.17 0.27 0.73 0.49 0.46 1.97 1.08
FAM189A1 ENST00000261275 85.66 38.62 63.24 0.27 0.72 0.49 0.46 1.66 1.36
IZUMO3 ENST00000543880 85.67 86.82 89.35 0.27 0.23 0.18 0.46 0.40 0.24
AC006486.1 ENST00000378108 85.67 90.65 91.11 0.27 0.25 0.15 0.46 0.36 0.20
RAB40AL ENST00000218249 85.68 92.01 91.65 0.27 0.24 0.14 0.46 0.33 0.18
MTIF3 ENST00000381116 85.68 82.86 87.44 0.27 0.32 0.28 0.46 0.49 0.31
NKD2 ENST00000296849 85.69 67.12 79.69 0.27 0.54 0.38 0.46 1.22 0.53
AHSG ENST00000411641 85.69 85.66 88.77 0.27 0.27 0.19 0.46 0.44 0.28
RGPD4 ENST00000408999 85.70 92.81 91.98 0.27 0.29 0.14 0.46 0.30 0.16
PATL2 ENST00000434130 85.70 55.50 73.41 0.27 0.57 0.42 0.46 1.61 0.77
C1orf228 ENST00000458657 85.71 48.94 69.51 0.27 0.65 0.44 0.46 2.04 0.97
KRTAP4-2 ENST00000377726 85.71 96.68 93.97 0.27 0.23 0.09 0.46 0.20 0.11
CCDC8 ENST00000307522 85.72 46.08 67.79 0.27 0.76 0.51 0.46 2.03 1.12
CASP12 ENST00000422698 85.72 61.59 76.79 0.27 0.54 0.35 0.45 1.41 0.61
MAPK15 ENST00000338033 85.73 81.06 86.61 0.27 0.35 0.30 0.45 0.55 0.33
MAGIX ENST00000412696 85.73 92.32 91.83 0.27 0.25 0.14 0.45 0.30 0.17
FAM207A ENST00000291634 85.74 52.28 71.53 0.27 0.62 0.44 0.45 1.84 0.84

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