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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
ZNF470 ENST00000330619 74.31 79.83 80.39 0.37 0.35 0.38 0.82 0.62 0.50
ZNF471 ENST00000308031 73.14 48.17 61.33 0.33 0.63 0.44 0.78 1.97 1.48
ZNF473 ENST00000595661 72.07 21.99 45.73 0.34 1.48 0.67 0.81 0.81 1.98
ZNF474 ENST00000296600 78.53 68.12 76.44 0.34 0.52 0.38 0.66 1.20 0.61
ZNF479 ENST00000331162 96.61 89.34 95.76 0.11 0.27 0.07 0.11 0.37 0.11
ZNF48 ENST00000320159 40.48 35.39 36.05 0.86 0.77 0.87 1.73 1.56 1.78
ZNF480 ENST00000595962 98.07 67.70 86.13 0.11 0.53 0.33 0.11 1.19 0.33
ZNF483 ENST00000309235 16.53 14.16 12.88 1.43 2.07 2.11 0.81 0.60 0.53
ZNF484 ENST00000395506 54.24 49.01 50.66 0.63 0.66 0.66 1.73 2.03 1.85
ZNF485 ENST00000361807 74.20 59.30 68.78 0.37 0.51 0.46 0.81 1.41 1.06
ZNF486 ENST00000335117 88.99 93.35 93.94 0.19 0.28 0.09 0.32 0.28 0.11
ZNF487 ENST00000437590 90.85 90.35 92.90 0.16 0.25 0.14 0.21 0.38 0.15
ZNF488 ENST00000395702 87.67 73.71 83.98 0.23 0.52 0.35 0.37 1.03 0.42
ZNF490 ENST00000311437 96.04 77.53 89.88 0.11 0.42 0.18 0.11 0.79 0.23
ZNF491 ENST00000323169 96.62 99.65 99.58 0.11 0.17 0.12 0.11 0.12 0.05
ZNF492 ENST00000456783 95.40 81.93 91.54 0.11 0.35 0.15 0.11 0.51 0.18
ZNF493 ENST00000392288 97.59 93.40 97.98 0.10 0.28 0.09 0.11 0.28 0.04
ZNF496 ENST00000294753 34.34 8.99 19.68 0.97 2.44 1.53 1.79 0.47 0.85
ZNF497 ENST00000311044 94.83 99.49 99.09 0.10 0.16 0.11 0.11 0.13 0.04
ZNF500 ENST00000219478 83.04 55.78 72.02 0.29 0.52 0.43 0.55 1.58 0.81
ZNF501 ENST00000396048 75.47 41.48 58.56 0.37 0.62 0.51 0.75 1.82 1.65
ZNF502 ENST00000296091 64.50 60.64 63.84 0.56 0.53 0.49 1.19 1.41 1.39
ZNF503 ENST00000372524 50.87 15.07 31.17 0.59 1.90 0.85 1.82 0.65 1.55
ZNF506 ENST00000443905 96.68 84.83 93.49 0.11 0.27 0.11 0.11 0.42 0.15
ZNF507 ENST00000311921 41.08 21.43 29.43 0.85 1.43 0.84 1.71 0.80 1.36

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