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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
GFRA3 ENST00000274721 27.64 30.94 27.42 1.24 1.05 0.96 1.43 1.35 1.27
ADAM19 ENST00000257527 27.64 23.59 23.71 1.24 1.39 1.15 1.43 0.93 1.02
TBCCD1 ENST00000424280 27.65 33.34 28.65 1.24 0.85 0.80 1.43 1.51 1.34
KIDINS220 ENST00000256707 27.65 15.75 19.74 1.24 1.87 1.52 1.43 0.69 0.85
RNF141 ENST00000265981 27.66 63.37 43.91 1.23 0.48 0.62 1.43 1.30 2.02
EIF2AK4 ENST00000263791 27.66 29.19 26.52 1.23 1.13 0.99 1.43 1.34 1.26
MFSD5 ENST00000534842 27.67 44.30 34.24 1.23 0.61 0.86 1.44 1.95 1.76
CD28 ENST00000324106 27.67 36.90 30.51 1.23 0.76 0.80 1.44 1.70 1.46
BCKDK ENST00000394951 27.68 45.44 34.78 1.23 0.68 0.90 1.44 1.99 1.76
DEAF1 ENST00000382409 27.68 34.47 29.21 1.23 0.80 0.82 1.44 1.56 1.33
GLT8D1 ENST00000407584 27.69 58.88 41.52 1.23 0.53 0.75 1.44 1.43 2.02
HSPA12A ENST00000369209 27.69 12.37 17.96 1.23 2.06 1.71 1.43 0.59 0.78
EPHB4 ENST00000358173 27.70 22.20 23.07 1.21 1.53 1.20 1.43 0.81 0.99
ADRA1B ENST00000306675 27.71 42.67 33.35 1.21 0.61 0.87 1.44 1.91 1.72
KDM4D ENST00000335080 27.71 82.89 54.84 1.21 0.32 0.52 1.44 0.49 1.74
LAMC1 ENST00000258341 27.72 5.47 14.33 1.23 3.04 2.00 1.44 0.33 0.60
POC1A ENST00000296484 27.72 50.70 37.46 1.23 0.63 0.86 1.44 1.94 2.01
MTCH2 ENST00000302503 27.73 31.16 27.57 1.23 1.01 0.96 1.44 1.36 1.26
TAB1 ENST00000216160 27.73 49.94 37.07 1.23 0.66 0.80 1.44 2.02 1.95
NXPH3 ENST00000328741 27.74 43.71 33.89 1.21 0.62 0.89 1.44 1.96 1.73
TMEM47 ENST00000275954 27.74 33.17 28.60 1.21 0.82 0.80 1.44 1.51 1.35
RASA3 ENST00000334062 27.75 35.75 29.94 1.20 0.78 0.86 1.44 1.58 1.45
PELI2 ENST00000267460 27.75 18.93 21.48 1.20 1.52 1.30 1.43 0.76 0.91
ALX1 ENST00000316824 27.76 30.76 27.40 1.20 1.06 0.96 1.44 1.37 1.27
ETFA ENST00000557943 27.76 34.94 29.54 1.20 0.76 0.84 1.44 1.54 1.38

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