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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
KIAA1984 ENST00000338005 82.13 54.48 70.61 0.30 0.59 0.43 0.57 1.66 0.91
PALM ENST00000338448 82.13 26.23 53.59 0.30 1.19 0.63 0.57 1.08 1.81
ZNF677 ENST00000333952 82.14 59.33 73.52 0.30 0.51 0.40 0.57 1.41 0.74
ATG9B ENST00000377974 82.14 62.72 75.34 0.30 0.51 0.37 0.57 1.31 0.65
LCE3E ENST00000368789 82.15 78.42 83.69 0.30 0.43 0.33 0.57 0.73 0.40
CRNN ENST00000271835 82.15 76.57 82.75 0.30 0.42 0.32 0.57 0.83 0.42
ATF5 ENST00000423777 82.16 42.17 63.27 0.30 0.62 0.49 0.57 1.87 1.36
HIST4H4 ENST00000539745 82.17 93.75 90.96 0.30 0.28 0.15 0.57 0.26 0.20
PABPC3 ENST00000281589 82.17 84.28 86.42 0.30 0.28 0.30 0.56 0.44 0.33
BAD ENST00000394532 82.18 80.07 84.43 0.30 0.37 0.33 0.56 0.60 0.40
MZF1 ENST00000215057 82.18 59.53 73.61 0.30 0.49 0.40 0.57 1.41 0.74
PLAC9 ENST00000372263 82.19 80.90 84.90 0.30 0.35 0.34 0.57 0.57 0.40
HEMGN ENST00000259456 82.19 65.54 76.99 0.30 0.53 0.37 0.57 1.22 0.61
FOXD4L1 ENST00000306507 82.20 71.68 80.26 0.30 0.52 0.37 0.57 1.07 0.51
FUT2 ENST00000425340 82.20 94.86 91.43 0.30 0.23 0.15 0.57 0.24 0.18
PIEZO1 ENST00000301015 82.21 28.96 55.15 0.30 1.15 0.51 0.57 1.31 1.74
C9 ENST00000263408 82.21 79.86 84.36 0.30 0.35 0.33 0.57 0.61 0.40
CCL8 ENST00000394620 82.22 87.62 88.08 0.30 0.23 0.23 0.57 0.35 0.30
IBA57 ENST00000366711 82.22 52.97 69.82 0.30 0.65 0.44 0.57 1.78 0.93
SNAPC4 ENST00000298532 82.23 53.23 69.96 0.30 0.66 0.47 0.57 1.75 0.92
NDUFA11 ENST00000418389 82.23 83.17 85.95 0.30 0.29 0.33 0.57 0.48 0.33
OASL ENST00000257570 82.24 82.56 85.71 0.30 0.34 0.33 0.57 0.51 0.33
PGBD3 ENST00000374127 82.24 87.39 87.96 0.30 0.23 0.24 0.57 0.41 0.32
OR8I2 ENST00000302124 82.25 91.93 90.14 0.30 0.23 0.18 0.57 0.33 0.21
OR8G5 ENST00000524943 82.25 80.15 84.54 0.30 0.37 0.34 0.57 0.59 0.39

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