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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
POMK ENST00000331373 45.46 80.77 64.39 0.57 0.37 0.51 1.76 0.57 1.33
DEFB124 ENST00000317676 45.46 92.34 71.42 0.57 0.25 0.46 1.76 0.30 0.87
KIAA0922 ENST00000409959 45.47 11.49 26.63 0.57 2.11 0.97 1.76 0.57 1.25
BNIP3 ENST00000368636 45.47 77.94 62.63 0.57 0.42 0.48 1.75 0.79 1.40
TBC1D1 ENST00000261439 45.48 37.07 39.63 0.57 0.78 0.80 1.75 1.67 2.04
CD81 ENST00000263645 45.48 16.93 29.39 0.57 1.66 0.84 1.75 0.71 1.36
TH ENST00000381178 45.49 40.46 41.18 0.57 0.62 0.76 1.75 1.77 2.02
PLOD1 ENST00000196061 45.49 48.91 45.89 0.57 0.63 0.70 1.75 2.04 1.98
BABAM1 ENST00000359435 45.50 14.07 27.95 0.57 2.07 0.84 1.76 0.59 1.28
QARS ENST00000306125 45.50 43.48 42.81 0.57 0.61 0.70 1.76 1.97 2.02
S100A13 ENST00000368699 45.51 84.31 66.61 0.57 0.28 0.52 1.76 0.44 1.20
PTCHD2 ENST00000294484 45.51 27.96 34.92 0.57 1.19 0.90 1.76 1.19 1.77
TOR1B ENST00000259339 45.52 35.17 38.61 0.57 0.76 0.84 1.75 1.58 2.01
VLDLR ENST00000382100 45.52 38.12 40.11 0.57 0.77 0.81 1.75 1.70 1.99
SAAL1 ENST00000524803 45.53 50.68 46.84 0.56 0.63 0.67 1.75 1.95 1.88
YBX3 ENST00000228251 45.53 52.36 47.78 0.56 0.62 0.65 1.75 1.82 1.88
CDC25C ENST00000323760 45.54 67.39 56.23 0.56 0.56 0.49 1.75 1.21 1.76
MGAT5B ENST00000428789 45.55 21.23 31.60 0.56 1.43 0.89 1.75 0.80 1.57
OCM2 ENST00000257627 45.55 76.87 61.95 0.56 0.43 0.48 1.75 0.81 1.46
SIMC1 ENST00000341199 45.56 48.70 45.83 0.56 0.63 0.68 1.74 1.99 1.97
CARTPT ENST00000296777 45.56 69.26 57.33 0.56 0.57 0.51 1.74 1.14 1.68
SCARB1 ENST00000261693 45.57 26.51 34.32 0.56 1.18 0.87 1.74 1.11 1.76
ELL ENST00000262809 45.57 9.24 25.49 0.56 2.47 1.02 1.75 0.47 1.19
CD19 ENST00000538922 45.58 16.13 29.02 0.56 1.82 0.82 1.75 0.69 1.31
LMBR1 ENST00000353442 45.58 45.59 43.98 0.56 0.75 0.61 1.75 1.99 2.03

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