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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
SLC12A1 ENST00000396577 40.42 43.99 40.47 0.86 0.61 0.80 1.74 1.97 2.04
RNF6 ENST00000381588 40.43 26.29 31.58 0.86 1.19 0.87 1.74 1.08 1.56
NHS ENST00000380060 40.43 0.79 18.57 0.86 4.11 1.59 1.73 0.27 0.81
HADHB ENST00000317799 40.44 56.41 47.17 0.86 0.52 0.67 1.73 1.53 1.89
GRINA ENST00000313269 40.44 25.45 31.17 0.86 1.25 0.85 1.73 1.05 1.55
ASB15 ENST00000451558 40.45 68.47 53.92 0.86 0.52 0.61 1.73 1.20 1.77
MCM5 ENST00000216122 40.45 30.16 33.46 0.86 1.10 0.89 1.73 1.40 1.72
CASQ2 ENST00000261448 40.46 75.65 58.13 0.86 0.44 0.48 1.73 0.90 1.65
PNPO ENST00000225573 40.46 78.94 60.13 0.86 0.40 0.47 1.73 0.69 1.61
HDAC11 ENST00000295757 40.47 35.77 36.24 0.86 0.78 0.85 1.73 1.58 1.84
RNF122 ENST00000256257 40.47 40.99 39.05 0.86 0.61 0.78 1.73 1.80 2.06
WDR53 ENST00000332629 40.48 46.90 41.92 0.86 0.71 0.68 1.73 1.94 2.01
ZNF48 ENST00000320159 40.48 35.39 36.05 0.86 0.77 0.87 1.73 1.56 1.78
LMCD1 ENST00000157600 40.49 40.49 38.77 0.86 0.62 0.82 1.73 1.77 2.03
AGR2 ENST00000419304 40.49 82.15 62.09 0.86 0.34 0.48 1.74 0.51 1.44
EFR3A ENST00000254624 40.50 38.76 37.88 0.86 0.70 0.85 1.75 1.67 2.01
SOCS6 ENST00000397942 40.50 6.87 21.80 0.86 2.62 1.23 1.75 0.37 0.94
COL25A1 ENST00000399132 40.51 45.56 41.25 0.86 0.75 0.75 1.75 1.99 2.01
RAB25 ENST00000361084 40.51 80.16 60.96 0.86 0.37 0.43 1.75 0.59 1.58
MN1 ENST00000302326 40.52 0.77 18.65 0.86 4.12 1.58 1.75 0.27 0.81
MOGS ENST00000233616 40.52 51.79 44.74 0.86 0.61 0.63 1.75 1.89 2.06
GMIP ENST00000203556 40.53 39.37 38.27 0.86 0.70 0.85 1.76 1.65 2.04
RGCC ENST00000379359 40.54 81.68 61.86 0.86 0.33 0.47 1.76 0.52 1.46
TMEM50B ENST00000542230 40.54 50.42 43.85 0.86 0.65 0.61 1.76 1.95 2.02
TRMT10C ENST00000309922 40.55 63.50 51.11 0.86 0.49 0.65 1.76 1.25 1.89

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