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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
ALKBH8 ENST00000428149 80.58 34.15 57.25 0.32 0.84 0.52 0.58 1.55 1.70
OR4N4 ENST00000328795 80.58 93.04 89.89 0.32 0.28 0.18 0.58 0.30 0.23
TAF7L ENST00000372907 80.59 11.03 44.27 0.32 2.10 0.61 0.58 0.52 2.05
PCDP1 ENST00000413369 80.60 48.29 66.12 0.32 0.63 0.51 0.58 1.99 1.21
ZSCAN22 ENST00000329665 80.60 67.87 77.44 0.32 0.52 0.35 0.58 1.18 0.57
DMBT1 ENST00000368909 80.61 59.67 72.88 0.32 0.52 0.40 0.58 1.39 0.81
LYAR ENST00000343470 80.61 58.99 72.48 0.32 0.52 0.44 0.58 1.42 0.83
CD14 ENST00000302014 80.62 81.21 84.20 0.32 0.34 0.34 0.58 0.55 0.42
AL163636.6 ENST00000553909 80.62 92.48 89.67 0.32 0.28 0.18 0.58 0.30 0.23
ZNF615 ENST00000594083 80.63 53.63 69.25 0.32 0.63 0.44 0.58 1.71 0.97
UBBP4 ENST00000578713 80.63 95.16 90.93 0.32 0.23 0.15 0.58 0.21 0.20
SLC52A1 ENST00000424747 80.64 77.77 82.60 0.32 0.42 0.32 0.58 0.79 0.43
TMEM255B ENST00000375353 80.64 84.59 85.91 0.32 0.28 0.33 0.58 0.42 0.33
PCDHB8 ENST00000239444 80.65 59.34 72.69 0.32 0.51 0.43 0.58 1.41 0.81
KPNA7 ENST00000327442 80.65 70.22 78.69 0.32 0.52 0.38 0.58 1.12 0.54
SPEM1 ENST00000323675 80.66 70.86 79.07 0.32 0.49 0.39 0.57 1.07 0.53
HIST1H2BA ENST00000274764 80.66 92.31 89.62 0.32 0.25 0.18 0.57 0.30 0.23
KRTAP5-1 ENST00000382171 80.67 74.65 81.01 0.32 0.54 0.39 0.57 0.98 0.50
OR8K1 ENST00000279783 80.67 94.65 90.71 0.32 0.23 0.15 0.57 0.24 0.20
HS3ST3A1 ENST00000284110 80.68 64.92 75.83 0.32 0.48 0.38 0.57 1.24 0.63
TMEM132C ENST00000435159 80.68 17.95 48.19 0.32 1.53 0.66 0.57 0.73 1.87
UTS2R ENST00000313135 80.69 95.47 91.02 0.32 0.24 0.15 0.57 0.21 0.20
HAS1 ENST00000222115 80.69 73.36 80.34 0.32 0.54 0.38 0.57 1.02 0.52
FAM217B ENST00000358293 80.70 99.34 92.85 0.32 0.16 0.14 0.57 0.12 0.15
PLIN3 ENST00000221957 80.70 65.05 75.89 0.32 0.51 0.38 0.57 1.24 0.62

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