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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
UBE2Q1 ENST00000292211 0.83 5.56 1.27 4.34 2.99 4.38 0.18 0.33 0.21
GNAL ENST00000334049 0.83 6.19 1.50 4.35 2.73 4.34 0.18 0.35 0.22
U2AF1 ENST00000291552 0.82 6.44 1.59 4.35 2.63 4.29 0.18 0.37 0.23
POU3F3 ENST00000361360 0.82 19.53 7.54 4.35 1.43 2.77 0.18 0.74 0.33
CAMK2B ENST00000395749 0.81 14.99 5.17 4.36 1.92 3.59 0.18 0.64 0.25
GADD45G ENST00000252506 0.81 37.97 17.25 4.36 0.77 1.64 0.18 1.71 0.74
YPEL2 ENST00000312655 0.80 15.51 5.49 4.36 1.87 3.43 0.18 0.67 0.26
MEAF6 ENST00000373075 0.80 34.03 15.17 4.37 0.82 1.83 0.19 1.55 0.64
GABRB3 ENST00000311550 0.79 14.38 4.84 4.35 2.05 3.67 0.19 0.61 0.24
ETS1 ENST00000392668 0.79 18.59 7.03 4.35 1.48 2.90 0.19 0.76 0.33
SUMO2 ENST00000420826 0.78 22.00 8.72 4.36 1.48 2.51 0.19 0.81 0.37
CDC73 ENST00000367435 0.77 5.39 1.21 4.36 3.05 4.42 0.19 0.33 0.21
EIF2S3 ENST00000253039 0.77 13.56 4.44 4.37 2.06 3.72 0.19 0.60 0.25
EIF4A3 ENST00000269349 0.76 1.73 0.26 4.37 3.84 4.84 0.19 0.26 0.18
TIAL1 ENST00000369093 0.76 1.47 0.21 4.37 3.91 4.86 0.19 0.26 0.18
GNAS ENST00000371100 0.75 16.75 6.00 4.36 1.68 3.28 0.19 0.71 0.30
CBX1 ENST00000393408 0.75 9.56 2.63 4.36 2.49 4.01 0.19 0.50 0.23
VCP ENST00000358901 0.74 2.10 0.32 4.36 3.69 4.83 0.19 0.28 0.18
RBM17 ENST00000446108 0.74 1.85 0.26 4.35 3.77 4.83 0.19 0.26 0.18
RPS5 ENST00000596046 0.73 13.60 4.46 4.35 2.05 3.71 0.19 0.59 0.25
CUL1 ENST00000325222 0.73 2.78 0.48 4.35 3.53 4.74 0.19 0.28 0.17
UHRF2 ENST00000276893 0.72 8.46 2.27 4.36 2.52 4.06 0.19 0.46 0.23
MAGOH ENST00000371470 0.72 23.98 9.88 4.36 1.37 2.30 0.19 0.95 0.41
HMGB1 ENST00000405805 0.71 23.03 9.32 4.37 1.44 2.32 0.19 0.91 0.38
UBE3A ENST00000397954 0.71 6.05 1.40 4.37 2.81 4.35 0.19 0.35 0.23

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