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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
ERF ENST00000222329 21.83 9.73 13.38 1.53 2.44 2.05 1.04 0.50 0.55
GLG1 ENST00000205061 21.83 6.29 11.67 1.53 2.71 2.23 1.04 0.36 0.47
AGPAT9 ENST00000395226 21.84 62.30 40.32 1.53 0.53 0.80 1.04 1.33 1.99
CCR4 ENST00000330953 21.84 53.76 35.91 1.53 0.63 0.86 1.04 1.71 1.79
NUDT3 ENST00000607016 21.85 33.84 25.97 1.53 0.85 0.99 1.04 1.56 1.25
LRRN3 ENST00000451085 21.85 35.90 27.05 1.53 0.80 0.99 1.04 1.58 1.29
SLC24A2 ENST00000341998 21.86 32.37 25.19 1.53 0.87 1.05 1.04 1.46 1.17
RERE ENST00000337907 21.86 1.80 9.30 1.53 3.80 2.32 1.03 0.26 0.38
SEC14L2 ENST00000312932 21.87 52.68 35.47 1.54 0.67 0.87 1.03 1.80 1.77
RELN ENST00000428762 21.87 3.80 10.41 1.54 3.31 2.18 1.03 0.31 0.43
GPR64 ENST00000379869 21.88 15.00 16.26 1.54 1.92 1.70 1.03 0.64 0.65
ANAPC10 ENST00000507656 21.88 58.04 38.26 1.54 0.53 0.85 1.03 1.45 2.04
LMNB1 ENST00000261366 21.89 19.41 18.64 1.53 1.46 1.58 1.03 0.74 0.81
PSKH1 ENST00000291041 21.89 33.70 25.96 1.53 0.84 0.99 1.03 1.56 1.25
SPOPL ENST00000280098 21.90 31.11 24.58 1.53 1.01 1.06 1.03 1.36 1.10
TXLNA ENST00000373609 21.90 8.10 12.54 1.53 2.52 2.20 1.03 0.44 0.51
PCID2 ENST00000246505 21.91 60.22 39.41 1.53 0.53 0.78 1.03 1.39 2.04
GPR174 ENST00000276077 21.92 38.17 28.23 1.53 0.77 0.81 1.03 1.71 1.29
DAZL ENST00000250863 21.92 8.59 12.79 1.52 2.52 2.11 1.03 0.47 0.52
SPRY2 ENST00000377102 21.93 10.53 13.92 1.52 2.18 2.07 1.03 0.50 0.59
ITGA6 ENST00000409080 21.93 25.62 21.89 1.52 1.24 1.19 1.03 1.05 0.96
TAF9 ENST00000328663 21.94 90.14 55.70 1.52 0.25 0.53 1.02 0.38 1.73
KATNAL1 ENST00000380615 21.94 22.06 20.06 1.52 1.49 1.49 1.03 0.81 0.86
RUVBL2 ENST00000595090 21.95 1.45 9.10 1.52 3.93 2.35 1.03 0.26 0.38
SEPT2 ENST00000391973 21.95 24.70 21.46 1.52 1.29 1.32 1.03 1.05 0.91

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