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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
HGD ENST00000283871 42.40 49.06 44.19 0.76 0.67 0.62 1.75 2.03 2.05
SESN2 ENST00000253063 42.42 49.09 44.20 0.76 0.66 0.62 1.75 2.04 2.05
LIMD2 ENST00000259006 42.46 42.66 40.73 0.76 0.59 0.81 1.75 1.90 2.05
SFXN5 ENST00000272433 42.61 42.26 40.62 0.76 0.61 0.81 1.77 1.88 2.05
LAP3 ENST00000226299 42.64 49.53 44.61 0.76 0.66 0.62 1.78 2.04 2.05
CHMP2A ENST00000600118 42.80 42.70 40.97 0.78 0.61 0.76 1.77 1.92 2.05
CCRN4L ENST00000280614 43.69 36.71 38.48 0.76 0.77 0.84 1.78 1.67 2.05
ZSCAN29 ENST00000396976 43.85 47.68 44.25 0.75 0.61 0.62 1.78 1.97 2.05
LGI3 ENST00000306317 43.88 41.13 40.66 0.73 0.59 0.81 1.78 1.82 2.05
CD274 ENST00000381577 43.89 41.83 41.07 0.73 0.59 0.75 1.77 1.80 2.05
MRPS22 ENST00000495075 43.95 48.43 44.77 0.75 0.63 0.65 1.77 2.02 2.05
GSTA4 ENST00000370963 43.97 48.44 44.76 0.75 0.63 0.65 1.77 2.02 2.05
FRZB ENST00000295113 44.06 48.61 45.00 0.73 0.63 0.70 1.78 2.00 2.05
ITGA7 ENST00000553804 44.19 41.22 40.91 0.71 0.61 0.78 1.75 1.83 2.05
GNAT3 ENST00000398291 44.41 48.35 45.01 0.66 0.63 0.70 1.77 2.00 2.05
PUS1 ENST00000376649 45.10 46.99 44.59 0.63 0.70 0.62 1.75 1.97 2.05
ZFYVE16 ENST00000338008 45.13 37.43 39.65 0.63 0.76 0.80 1.74 1.66 2.05
HIATL1 ENST00000375344 45.33 35.05 38.47 0.62 0.76 0.84 1.76 1.58 2.05
MME ENST00000460393 45.45 46.89 44.77 0.57 0.71 0.65 1.75 1.94 2.05
FOSL1 ENST00000312562 46.78 38.70 40.95 0.56 0.70 0.77 1.81 1.67 2.05
EFNA3 ENST00000368408 47.04 34.09 38.88 0.56 0.84 0.80 1.81 1.53 2.05
TBC1D2 ENST00000375066 47.38 44.23 44.28 0.56 0.62 0.61 1.82 1.95 2.05
LDLRAD3 ENST00000315571 48.29 43.94 44.70 0.56 0.61 0.62 1.82 1.97 2.05
GZF1 ENST00000338121 49.91 30.46 38.47 0.53 1.09 0.84 1.81 1.38 2.05
CDH13 ENST00000268613 49.99 30.45 38.50 0.54 1.09 0.84 1.80 1.38 2.05

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