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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
AGPS ENST00000264167 5.24 1.62 1.44 3.42 3.86 4.32 0.32 0.26 0.23
DPYSL5 ENST00000288699 13.27 1.59 4.76 1.67 3.86 3.67 0.66 0.26 0.25
PRKAR1A ENST00000589228 1.82 1.62 0.45 4.29 3.86 4.74 0.22 0.26 0.17
SCN8A ENST00000354534 0.20 1.58 0.12 4.50 3.87 4.87 0.16 0.26 0.18
DNMT1 ENST00000359526 4.46 1.61 1.19 3.71 3.87 4.44 0.29 0.26 0.21
TRIM24 ENST00000343526 2.17 1.58 0.53 4.16 3.87 4.70 0.27 0.26 0.17
UBA1 ENST00000335972 14.16 1.61 5.15 1.62 3.87 3.59 0.71 0.26 0.25
NRXN3 ENST00000554719 6.72 1.57 1.95 2.99 3.87 4.13 0.37 0.26 0.24
MYCBP2 ENST00000544440 7.25 1.57 2.12 2.91 3.88 4.09 0.38 0.26 0.23
WAPAL ENST00000298767 2.86 1.56 0.72 3.95 3.88 4.58 0.30 0.26 0.20
AGO2 ENST00000220592 2.69 1.55 0.65 4.02 3.88 4.64 0.29 0.26 0.19
RIF1 ENST00000243326 31.26 1.52 14.10 0.96 3.88 2.05 1.69 0.26 0.60
TIPARP ENST00000461166 9.64 1.55 3.02 2.15 3.88 3.96 0.48 0.26 0.24
RBM26 ENST00000267229 13.06 1.51 4.62 1.70 3.89 3.69 0.64 0.26 0.25
EIF4G3 ENST00000602326 8.53 1.54 2.58 2.45 3.89 4.01 0.44 0.26 0.23
ANKHD1 ENST00000297183 9.61 1.51 2.99 2.15 3.89 3.98 0.48 0.26 0.24
ISY1 ENST00000273541 16.49 1.54 6.33 1.44 3.89 3.10 0.81 0.26 0.32
PRRC2C ENST00000338920 25.82 1.50 11.36 1.34 3.89 2.20 1.21 0.26 0.45
AP2A2 ENST00000448903 30.66 1.53 13.74 0.96 3.89 2.06 1.63 0.26 0.57
USP8 ENST00000433963 16.29 1.50 6.15 1.48 3.90 3.20 0.80 0.26 0.30
ANKHD1-EIF4EBP3 ENST00000532219 9.62 1.53 3.01 2.15 3.90 3.97 0.48 0.26 0.24
RORB ENST00000376896 3.92 1.49 1.00 3.81 3.90 4.45 0.30 0.26 0.21
NOTCH2 ENST00000256646 11.17 1.52 3.72 1.81 3.90 3.80 0.59 0.26 0.23
ZMYM3 ENST00000353904 5.27 1.49 1.41 3.40 3.90 4.34 0.32 0.26 0.23
PSMD3 ENST00000264639 18.47 1.48 7.34 1.54 3.91 2.81 0.91 0.26 0.34

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