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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
CETN3 ENST00000283122 22.73 77.14 48.82 1.44 0.42 0.70 1.05 0.78 1.86
POLR1A ENST00000263857 22.74 8.34 13.14 1.44 2.51 2.10 1.05 0.46 0.52
GLUL ENST00000311223 22.74 5.04 11.56 1.44 3.21 2.21 1.05 0.32 0.45
ZSCAN12 ENST00000361028 22.75 45.97 32.56 1.44 0.76 0.89 1.05 2.02 1.62
MTX2 ENST00000249442 22.75 34.61 26.84 1.44 0.80 0.97 1.05 1.54 1.27
SENP7 ENST00000394095 22.76 15.01 16.75 1.44 1.91 1.70 1.05 0.64 0.70
KATNA1 ENST00000367411 22.76 36.27 27.66 1.44 0.82 0.95 1.05 1.61 1.27
EDA ENST00000374552 22.77 10.55 14.41 1.43 2.16 2.01 1.05 0.52 0.59
ANAPC2 ENST00000323927 22.77 4.39 11.25 1.43 3.26 2.16 1.05 0.32 0.45
CCDC50 ENST00000392456 22.78 38.80 28.93 1.43 0.70 0.81 1.06 1.66 1.31
ZDHHC5 ENST00000287169 22.78 0.84 9.28 1.43 4.10 2.32 1.06 0.28 0.38
PCDH7 ENST00000543491 22.79 19.40 19.08 1.44 1.46 1.54 1.05 0.74 0.85
TMEM87A ENST00000389834 22.79 20.80 19.84 1.44 1.44 1.48 1.05 0.81 0.85
ITM2B ENST00000378565 22.80 26.75 22.93 1.44 1.21 1.19 1.05 1.12 0.98
DHX38 ENST00000268482 22.80 32.86 25.97 1.44 0.84 0.99 1.05 1.44 1.25
FAM91A1 ENST00000334705 22.81 24.08 21.58 1.44 1.37 1.28 1.05 0.97 0.93
RNF170 ENST00000534961 22.81 26.32 22.73 1.44 1.19 1.18 1.05 1.08 0.98
CDH11 ENST00000268603 22.82 3.68 10.86 1.44 3.34 2.19 1.05 0.31 0.44
RTFDC1 ENST00000023939 22.82 44.00 31.62 1.44 0.61 0.89 1.05 1.97 1.57
NT5C2 ENST00000343289 22.83 37.91 28.52 1.44 0.80 0.78 1.06 1.70 1.31
PLEK ENST00000234313 22.83 42.34 30.85 1.44 0.61 0.78 1.06 1.90 1.49
PPAPDC1A ENST00000398250 22.84 54.69 37.00 1.44 0.58 0.78 1.06 1.65 1.95
L3MBTL3 ENST00000529410 22.84 8.23 13.13 1.44 2.58 2.10 1.06 0.45 0.52
CNTNAP1 ENST00000264638 22.85 20.71 19.83 1.44 1.47 1.49 1.06 0.80 0.85
SDHC ENST00000367975 22.86 69.08 44.50 1.44 0.56 0.61 1.06 1.14 2.04

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