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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
ABCC6 ENST00000205557 69.25 56.54 64.17 0.54 0.52 0.51 0.98 1.54 1.36
ABCC5 ENST00000334444 12.42 17.15 12.38 1.64 1.61 2.23 0.63 0.75 0.50
ABCC4 ENST00000376887 34.27 24.90 27.74 0.96 1.32 0.91 1.78 1.07 1.27
ABCC3 ENST00000285238 54.89 49.29 51.15 0.63 0.65 0.65 1.71 2.02 1.90
ABCC2 ENST00000370449 56.58 63.74 60.70 0.58 0.49 0.44 1.63 1.22 1.61
ABCC12 ENST00000311303 57.69 70.38 65.59 0.57 0.52 0.51 1.53 1.09 1.29
ABCC11 ENST00000394747 78.95 67.32 76.21 0.32 0.56 0.37 0.64 1.21 0.62
ABCC10 ENST00000372530 46.13 54.13 49.00 0.58 0.63 0.72 1.81 1.68 1.84
ABCC1 ENST00000399410 43.10 17.53 28.49 0.82 1.58 0.78 1.78 0.73 1.29
ABCB9 ENST00000542678 58.78 33.43 44.68 0.56 0.84 0.62 1.48 1.52 2.06
ABCB8 ENST00000358849 60.60 61.05 61.48 0.58 0.54 0.44 1.34 1.39 1.48
ABCB7 ENST00000253577 10.91 1.29 3.52 1.90 3.96 3.83 0.57 0.27 0.23
ABCB6 ENST00000265316 66.37 55.06 61.38 0.59 0.58 0.44 1.06 1.63 1.48
ABCB5 ENST00000404938 71.27 61.27 68.26 0.40 0.53 0.52 0.85 1.39 1.08
ABCB4 ENST00000265723 24.18 24.76 22.62 1.34 1.32 1.18 1.13 1.05 0.96
ABCB11 ENST00000263817 26.21 32.80 27.65 1.34 0.84 0.95 1.27 1.44 1.27
ABCB10 ENST00000344517 47.89 54.16 50.02 0.53 0.63 0.61 1.80 1.68 1.92
ABCB1 ENST00000265724 28.52 23.38 24.00 1.16 1.40 1.10 1.53 0.93 1.05
ABCA9 ENST00000340001 61.90 57.01 59.84 0.71 0.56 0.49 1.30 1.51 1.63
ABCA8 ENST00000269080 76.71 65.35 73.83 0.33 0.52 0.42 0.73 1.25 0.71
ABCA7 ENST00000263094 79.38 58.30 71.32 0.34 0.54 0.43 0.58 1.43 0.87
ABCA6 ENST00000284425 79.42 45.59 63.74 0.34 0.75 0.49 0.58 1.99 1.38
ABCA5 ENST00000392676 48.56 43.45 44.54 0.51 0.61 0.62 1.80 1.96 2.04
ABCA4 ENST00000370225 43.14 49.68 45.07 0.82 0.66 0.70 1.79 2.02 2.02
ABCA3 ENST00000301732 50.79 25.13 36.06 0.59 1.32 0.87 1.83 1.03 1.79

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