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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
ZNF510 ENST00000375231 74.31 51.91 64.37 0.37 0.61 0.51 0.82 1.86 1.34
ZNF511 ENST00000361518 66.05 72.22 71.70 0.59 0.51 0.46 1.05 1.04 0.82
ZNF512 ENST00000355467 11.51 12.97 9.75 1.72 2.07 2.28 0.59 0.59 0.40
ZNF512B ENST00000450537 49.28 6.06 25.79 0.57 2.81 1.02 1.80 0.35 1.23
ZNF513 ENST00000323703 20.98 19.57 18.23 1.54 1.43 1.64 1.01 0.74 0.79
ZNF514 ENST00000295208 68.34 76.55 75.37 0.56 0.42 0.37 0.99 0.83 0.66
ZNF516 ENST00000443185 20.48 4.17 9.85 1.53 3.26 2.30 1.03 0.32 0.40
ZNF517 ENST00000359971 88.06 72.72 83.77 0.20 0.48 0.34 0.35 1.03 0.41
ZNF518B ENST00000326756 64.51 28.98 45.45 0.56 1.15 0.70 1.19 1.31 1.99
ZNF519 ENST00000590202 89.24 90.53 92.62 0.18 0.25 0.14 0.32 0.37 0.15
ZNF521 ENST00000361524 8.81 1.04 2.52 2.42 4.06 4.01 0.45 0.28 0.24
ZNF524 ENST00000591046 82.05 75.79 82.28 0.30 0.43 0.34 0.57 0.88 0.45
ZNF525 ENST00000474037 88.72 76.62 85.94 0.19 0.42 0.33 0.33 0.83 0.33
ZNF526 ENST00000301215 60.63 24.42 40.67 0.58 1.30 0.81 1.34 1.00 2.04
ZNF527 ENST00000436120 56.71 36.18 45.11 0.56 0.82 0.70 1.60 1.61 2.01
ZNF528 ENST00000360465 96.07 81.60 91.65 0.11 0.33 0.14 0.11 0.52 0.18
ZNF529 ENST00000591340 73.91 47.18 61.15 0.35 0.66 0.43 0.81 2.00 1.50
ZNF530 ENST00000332854 98.18 90.08 96.91 0.11 0.25 0.08 0.11 0.37 0.07
ZNF532 ENST00000336078 11.58 12.24 9.37 1.73 2.06 2.30 0.59 0.58 0.39
ZNF534 ENST00000332323 97.73 93.97 98.19 0.10 0.25 0.09 0.10 0.26 0.05
ZNF536 ENST00000355537 1.58 7.12 2.08 4.25 2.58 4.09 0.20 0.37 0.23
ZNF540 ENST00000592533 95.11 52.17 76.75 0.10 0.62 0.34 0.12 1.84 0.61
ZNF541 ENST00000314121 76.38 3.54 38.25 0.33 3.38 0.85 0.74 0.30 2.04
ZNF543 ENST00000321545 94.60 85.59 92.85 0.10 0.27 0.14 0.12 0.44 0.15
ZNF544 ENST00000269829 96.41 82.84 92.31 0.10 0.32 0.14 0.11 0.49 0.15

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