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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
PSME1 ENST00000382708 32.80 36.34 32.75 0.94 0.82 0.86 1.70 1.62 1.65
GINS4 ENST00000276533 32.81 58.63 44.18 0.94 0.54 0.62 1.70 1.42 2.05
SLC12A9 ENST00000354161 32.81 65.43 47.97 0.94 0.53 0.67 1.70 1.25 1.88
FBXO4 ENST00000281623 32.82 59.06 44.45 0.94 0.49 0.61 1.70 1.43 2.04
RNF34 ENST00000392465 32.82 24.07 26.56 0.94 1.37 0.99 1.70 0.97 1.25
IDH3G ENST00000217901 32.83 36.95 33.04 0.94 0.75 0.85 1.70 1.70 1.66
NRIP3 ENST00000309166 32.83 82.10 57.36 0.94 0.34 0.51 1.70 0.50 1.67
MEGF8 ENST00000334370 32.84 15.89 22.56 0.94 1.89 1.16 1.70 0.68 0.97
CHCHD10 ENST00000484558 32.84 92.63 64.03 0.94 0.29 0.53 1.70 0.31 1.39
TPI1 ENST00000229270 32.85 42.39 35.74 0.94 0.59 0.85 1.70 1.90 1.78
C19orf66 ENST00000253110 32.85 28.23 28.68 0.94 1.19 0.80 1.70 1.22 1.34
CNPY2 ENST00000273308 32.86 53.82 41.58 0.94 0.63 0.73 1.70 1.71 2.01
ABRACL ENST00000367660 32.87 74.04 52.77 0.94 0.53 0.61 1.70 1.03 1.89
GPER1 ENST00000397092 32.87 36.18 32.70 0.94 0.82 0.86 1.70 1.61 1.64
C1QBP ENST00000225698 32.88 82.51 57.66 0.94 0.34 0.51 1.70 0.52 1.67
CHN1 ENST00000409900 32.88 27.06 28.15 0.94 1.23 0.82 1.70 1.12 1.27
WDR63 ENST00000294664 32.89 42.14 35.64 0.94 0.61 0.85 1.70 1.87 1.77
FSCN1 ENST00000382361 32.89 20.96 24.98 0.94 1.44 1.04 1.70 0.83 1.14
ZSCAN20 ENST00000361328 32.90 25.59 27.37 0.94 1.25 0.96 1.70 1.05 1.27
CREB3L1 ENST00000529193 32.90 12.46 20.84 0.94 2.06 1.46 1.70 0.59 0.88
HIST3H2A ENST00000366695 32.91 70.07 50.50 0.94 0.53 0.67 1.70 1.14 1.86
INHBB ENST00000295228 32.91 11.17 20.10 0.94 2.09 1.49 1.71 0.54 0.85
FHOD3 ENST00000257209 32.92 17.45 23.27 0.94 1.59 1.19 1.71 0.74 1.00
RPN2 ENST00000237530 32.92 22.13 25.61 0.94 1.52 1.05 1.72 0.83 1.21
CAP1 ENST00000372797 32.93 29.32 29.28 0.94 1.13 0.84 1.72 1.36 1.34

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