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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
ASIP ENST00000568305 74.38 81.38 81.24 0.37 0.33 0.38 0.82 0.54 0.49
KCTD14 ENST00000353172 74.39 88.45 84.76 0.37 0.23 0.34 0.82 0.37 0.40
TMPRSS2 ENST00000398585 74.39 47.53 61.72 0.37 0.62 0.46 0.81 2.01 1.46
NPFF ENST00000267017 74.40 94.37 87.51 0.37 0.23 0.28 0.81 0.24 0.30
TRIM50 ENST00000333149 74.40 67.98 73.99 0.37 0.52 0.39 0.81 1.19 0.70
OR6C74 ENST00000343870 74.41 83.74 82.45 0.37 0.27 0.33 0.81 0.47 0.44
CCDC54 ENST00000261058 74.41 95.11 87.89 0.37 0.23 0.24 0.81 0.21 0.32
CHP2 ENST00000300113 74.42 80.46 80.74 0.37 0.37 0.39 0.81 0.59 0.52
PROX2 ENST00000556084 74.42 90.00 85.57 0.37 0.25 0.32 0.81 0.37 0.35
ACTRT2 ENST00000378404 74.43 76.40 78.66 0.37 0.43 0.38 0.81 0.86 0.55
CLDN20 ENST00000367165 74.43 94.28 87.49 0.37 0.24 0.28 0.81 0.25 0.30
MMP21 ENST00000368808 74.44 64.08 71.85 0.37 0.49 0.44 0.81 1.20 0.83
GSTM5 ENST00000256593 74.44 79.68 80.38 0.37 0.37 0.38 0.81 0.65 0.50
LHB ENST00000221421 74.45 90.24 85.66 0.37 0.25 0.33 0.81 0.38 0.34
MAGEE1 ENST00000361470 74.45 13.86 42.40 0.37 2.05 0.68 0.81 0.60 2.01
CENPM ENST00000215980 74.46 51.86 64.45 0.37 0.59 0.51 0.80 1.87 1.34
ARMC6 ENST00000535612 74.46 68.40 74.29 0.37 0.52 0.39 0.80 1.21 0.70
CDKL3 ENST00000265334 74.47 63.64 71.59 0.37 0.49 0.44 0.80 1.23 0.83
ERCC6-PGBD3 ENST00000515869 74.47 43.56 59.22 0.37 0.61 0.49 0.80 1.96 1.68
CYP7B1 ENST00000310193 74.48 51.24 64.13 0.37 0.65 0.52 0.80 1.89 1.37
IRX4 ENST00000505790 74.48 33.75 53.54 0.37 0.84 0.63 0.80 1.56 1.81
GNG7 ENST00000382159 74.49 75.09 78.00 0.37 0.51 0.38 0.80 0.91 0.54
BCAS1 ENST00000395961 74.50 45.50 60.52 0.37 0.71 0.44 0.80 1.99 1.58
GPR113 ENST00000311519 74.50 65.36 72.64 0.37 0.52 0.46 0.80 1.25 0.81
C9orf135 ENST00000377197 74.51 78.41 79.77 0.37 0.43 0.38 0.79 0.73 0.53

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