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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
CD99 ENST00000381192 88.33 50.96 72.35 0.20 0.65 0.44 0.35 1.92 0.82
RIMBP3 ENST00000426804 88.33 81.11 87.83 0.20 0.35 0.24 0.35 0.55 0.32
YBEY ENST00000329319 88.34 94.56 94.20 0.20 0.23 0.09 0.35 0.24 0.12
TSPAN6 ENST00000373020 88.34 55.42 74.77 0.20 0.58 0.40 0.35 1.60 0.66
MSLN ENST00000382862 88.35 75.80 85.43 0.20 0.43 0.34 0.35 0.88 0.35
CHST13 ENST00000319340 88.35 87.27 90.88 0.20 0.22 0.15 0.35 0.41 0.20
ASCL4 ENST00000342331 88.36 90.53 92.12 0.20 0.25 0.14 0.35 0.37 0.16
CFC1 ENST00000259216 88.36 71.42 83.26 0.20 0.53 0.29 0.35 1.05 0.40
BRICD5 ENST00000328540 88.37 96.77 95.28 0.20 0.23 0.08 0.35 0.19 0.10
APOBR ENST00000564831 88.37 39.17 65.23 0.20 0.70 0.53 0.35 1.61 1.31
RNASEL ENST00000367559 88.38 62.42 78.67 0.20 0.53 0.38 0.35 1.32 0.55
C2orf91 ENST00000378711 88.38 83.31 88.95 0.20 0.27 0.19 0.35 0.48 0.28
MARCO ENST00000327097 88.39 75.18 85.14 0.20 0.49 0.33 0.35 0.91 0.37
PTPRH ENST00000376350 88.39 65.94 80.50 0.20 0.54 0.39 0.35 1.23 0.51
C3orf55 ENST00000449199 88.40 87.96 91.13 0.20 0.25 0.15 0.35 0.37 0.19
SPINK14 ENST00000356972 88.40 74.61 84.87 0.20 0.54 0.34 0.35 0.99 0.40
MEPE ENST00000424957 88.41 69.40 82.26 0.20 0.56 0.34 0.35 1.14 0.45
KRTAP5-7 ENST00000398536 88.41 93.38 93.69 0.20 0.28 0.11 0.35 0.28 0.14
PRSS55 ENST00000328655 88.42 93.35 93.65 0.20 0.28 0.13 0.35 0.28 0.15
DUSP28 ENST00000405954 88.43 84.08 89.35 0.20 0.27 0.18 0.35 0.45 0.24
CD3EAP ENST00000309424 88.43 90.40 92.09 0.20 0.25 0.14 0.35 0.37 0.16
C6orf223 ENST00000336600 88.44 89.25 91.67 0.20 0.27 0.14 0.35 0.36 0.18
GZMB ENST00000216341 88.44 94.57 94.25 0.20 0.23 0.10 0.35 0.24 0.12
POMZP3 ENST00000310842 88.45 74.70 84.93 0.20 0.54 0.34 0.35 0.96 0.40
WFDC6 ENST00000372670 88.45 92.79 93.32 0.20 0.29 0.13 0.35 0.30 0.15

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