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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
METTL3 ENST00000298717 5.69 42.80 22.44 3.19 0.63 1.15 0.33 1.92 0.97
FOXP1 ENST00000491238 5.69 4.66 2.68 3.19 3.26 4.00 0.33 0.31 0.23
RPL9 ENST00000449470 5.70 11.86 6.04 3.19 2.10 3.29 0.33 0.58 0.30
RPL11 ENST00000374550 5.70 15.08 7.75 3.18 1.90 2.66 0.33 0.65 0.33
POLR2H ENST00000456318 5.71 32.42 16.93 3.16 0.87 1.67 0.33 1.48 0.71
NOVA2 ENST00000263257 5.71 8.65 4.47 3.16 2.49 3.70 0.33 0.47 0.25
NR2C2 ENST00000323373 5.72 7.16 3.78 3.16 2.58 3.79 0.33 0.37 0.24
PDHA1 ENST00000379806 5.72 9.47 4.86 3.16 2.48 3.67 0.33 0.49 0.24
UNC79 ENST00000256339 5.73 2.81 2.02 3.16 3.52 4.11 0.33 0.28 0.23
AGPAT6 ENST00000396987 5.73 26.34 13.70 3.16 1.19 2.04 0.34 1.08 0.58
CADM2 ENST00000405615 5.74 17.77 9.19 3.16 1.53 2.32 0.34 0.72 0.38
NR5A1 ENST00000373588 5.74 9.63 4.96 3.16 2.47 3.68 0.34 0.50 0.25
PRKCA ENST00000413366 5.75 18.56 9.65 3.18 1.49 2.26 0.34 0.76 0.40
CNR1 ENST00000537554 5.75 30.88 16.13 3.18 1.08 1.71 0.34 1.36 0.66
LGI1 ENST00000371418 5.76 4.92 2.77 3.18 3.25 4.04 0.34 0.31 0.24
PI4K2A ENST00000370631 5.76 18.69 9.72 3.18 1.52 2.28 0.34 0.75 0.40
CRK ENST00000300574 5.77 14.52 7.54 3.18 2.04 2.77 0.34 0.61 0.33
NR4A3 ENST00000330847 5.77 16.60 8.53 3.18 1.76 2.51 0.33 0.71 0.37
RXRB ENST00000374685 5.78 6.98 3.75 3.18 2.59 3.79 0.33 0.37 0.24
LRRC3B ENST00000396641 5.78 44.87 23.42 3.18 0.68 1.19 0.33 1.99 1.01
C16orf87 ENST00000285697 5.79 61.98 32.06 3.18 0.56 0.90 0.33 1.36 1.60
CIC ENST00000575354 5.80 5.13 2.87 3.18 3.21 4.00 0.33 0.33 0.23
RUFY3 ENST00000381006 5.80 22.06 11.61 3.18 1.49 2.23 0.33 0.81 0.45
NLK ENST00000407008 5.81 1.87 1.74 3.18 3.76 4.23 0.33 0.26 0.23
BUB3 ENST00000368865 5.81 19.23 10.09 3.18 1.47 2.25 0.33 0.75 0.43

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