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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
C19orf26 ENST00000590083 85.33 24.04 54.20 0.28 1.37 0.59 0.47 0.96 1.74
ZNF226 ENST00000590089 76.92 64.81 73.65 0.33 0.48 0.40 0.73 1.24 0.74
ZNF519 ENST00000590202 89.24 90.53 92.62 0.18 0.25 0.14 0.32 0.37 0.15
MBD1 ENST00000590208 19.54 10.54 12.59 1.57 2.18 2.20 1.00 0.51 0.52
ELANE ENST00000590230 86.09 61.10 76.69 0.25 0.53 0.34 0.43 1.39 0.60
PDCD5 ENST00000590247 37.91 65.23 50.60 0.92 0.51 0.66 1.73 1.24 1.85
S1PR2 ENST00000590320 40.02 59.09 48.45 0.86 0.49 0.68 1.75 1.43 1.87
APOC2 ENST00000590360 98.09 49.24 76.79 0.11 0.66 0.35 0.11 2.02 0.61
ZNF573 ENST00000590414 77.88 69.39 76.73 0.32 0.56 0.34 0.67 1.14 0.60
MAP2K6 ENST00000590474 2.80 12.29 4.81 3.98 2.06 3.67 0.28 0.59 0.24
TMC6 ENST00000590602 59.21 37.96 47.33 0.54 0.78 0.66 1.46 1.70 1.87
ZNF763 ENST00000590798 97.67 76.99 90.37 0.10 0.43 0.15 0.10 0.79 0.21
GIPR ENST00000590918 71.40 87.38 82.78 0.37 0.23 0.32 0.83 0.41 0.42
COASY ENST00000590958 52.91 59.95 56.16 0.65 0.53 0.49 1.78 1.37 1.77
POLR2J2 ENST00000591000 89.98 95.73 95.72 0.18 0.23 0.07 0.27 0.20 0.11
PLEKHH3 ENST00000591022 69.75 40.17 54.51 0.53 0.61 0.57 0.95 1.73 1.75
ZNF524 ENST00000591046 82.05 75.79 82.28 0.30 0.43 0.34 0.57 0.88 0.45
ASNA1 ENST00000591090 7.74 17.91 10.39 2.72 1.54 2.19 0.40 0.73 0.43
PPY ENST00000591228 37.99 85.74 62.86 0.92 0.27 0.51 1.72 0.44 1.40
LSM12 ENST00000591247 4.43 10.25 4.68 3.70 2.28 3.69 0.29 0.49 0.25
ZNF529 ENST00000591340 73.91 47.18 61.15 0.35 0.66 0.43 0.81 2.00 1.50
ZNF850 ENST00000591344 99.56 38.33 71.46 0.12 0.75 0.46 0.13 1.72 0.86
WBP2 ENST00000591399 63.39 30.64 45.69 0.59 1.06 0.68 1.23 1.38 2.00
CCDC68 ENST00000591504 71.84 74.90 76.49 0.34 0.53 0.38 0.81 0.95 0.61
MAP4K1 ENST00000591517 17.33 12.15 12.34 1.47 2.07 2.25 0.87 0.57 0.50

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