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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
LDLR ENST00000558518 66.63 62.53 66.26 0.62 0.53 0.52 1.05 1.31 1.20
AMER2 ENST00000515384 66.64 37.61 51.16 0.62 0.78 0.63 1.05 1.70 1.90
ZNF791 ENST00000343325 66.64 27.92 45.99 0.62 1.19 0.70 1.05 1.19 1.97
BPIFB6 ENST00000349552 66.65 70.58 71.02 0.62 0.52 0.43 1.05 1.09 0.85
MSANTD1 ENST00000438480 66.65 24.67 44.08 0.62 1.29 0.61 1.05 1.04 2.04
BRF2 ENST00000220659 66.66 64.85 67.58 0.62 0.48 0.51 1.05 1.25 1.13
SLCO1A2 ENST00000307378 66.66 72.90 72.47 0.62 0.49 0.44 1.05 1.03 0.82
KCNJ16 ENST00000392670 66.67 84.79 79.04 0.62 0.27 0.39 1.05 0.42 0.53
POLM ENST00000242248 66.68 61.63 65.76 0.62 0.54 0.51 1.05 1.39 1.26
FSIP1 ENST00000350221 66.68 71.08 71.39 0.62 0.49 0.44 1.05 1.07 0.87
ZP3 ENST00000394857 66.69 49.34 58.07 0.62 0.65 0.47 1.05 2.02 1.66
USMG5 ENST00000369825 66.69 86.09 79.67 0.62 0.27 0.38 1.05 0.44 0.53
CLDN8 ENST00000399899 66.70 82.34 77.71 0.62 0.34 0.38 1.05 0.52 0.55
HSD3B2 ENST00000543831 66.70 81.57 77.30 0.62 0.33 0.35 1.05 0.52 0.58
PRDX3 ENST00000298510 66.71 47.58 57.01 0.62 0.61 0.51 1.05 2.00 1.70
PRLHR ENST00000239032 66.71 77.38 74.99 0.62 0.42 0.40 1.05 0.76 0.66
CCDC157 ENST00000405659 66.72 74.48 73.40 0.62 0.53 0.42 1.05 0.99 0.77
SLC39A11 ENST00000542342 66.72 88.46 80.94 0.62 0.23 0.39 1.05 0.36 0.50
NXPE4 ENST00000375478 66.73 81.04 77.04 0.62 0.35 0.37 1.05 0.55 0.61
CSF3 ENST00000225474 66.73 39.64 52.48 0.61 0.68 0.61 1.05 1.65 1.91
JPH3 ENST00000284262 66.74 6.17 34.68 0.61 2.76 0.90 1.05 0.35 1.75
SH3YL1 ENST00000356150 66.74 61.98 65.99 0.61 0.56 0.51 1.05 1.36 1.22
NEIL1 ENST00000564784 66.75 55.61 61.91 0.61 0.53 0.48 1.05 1.59 1.45
UGT1A5 ENST00000373414 66.75 69.83 70.60 0.61 0.54 0.43 1.05 1.14 0.90
OR1J1 ENST00000259357 66.76 91.45 82.52 0.61 0.23 0.33 1.05 0.33 0.43

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