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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
C14orf105 ENST00000216445 51.78 45.34 47.31 0.58 0.68 0.66 1.82 1.99 1.87
CUEDC1 ENST00000577830 51.79 62.54 57.04 0.58 0.53 0.51 1.82 1.31 1.70
PRSS12 ENST00000296498 51.79 68.45 60.66 0.58 0.52 0.44 1.82 1.20 1.61
HHAT ENST00000545154 51.80 46.43 47.94 0.58 0.73 0.66 1.82 2.03 1.88
PAH ENST00000553106 51.81 79.00 67.17 0.58 0.40 0.52 1.82 0.70 1.17
RNF216 ENST00000389902 51.81 28.99 38.66 0.58 1.15 0.82 1.82 1.31 2.01
C1orf192 ENST00000367974 51.82 84.75 70.58 0.58 0.27 0.43 1.82 0.42 0.90
RDH5 ENST00000257895 51.82 83.66 69.98 0.59 0.27 0.47 1.82 0.47 0.92
FKBP14 ENST00000222803 51.83 84.62 70.53 0.59 0.27 0.43 1.82 0.42 0.91
TLR6 ENST00000436693 51.83 45.20 47.27 0.59 0.70 0.66 1.81 1.98 1.87
STAP1 ENST00000265404 51.84 57.53 54.21 0.61 0.57 0.59 1.81 1.48 1.75
RBM38 ENST00000356208 51.84 29.21 38.82 0.61 1.13 0.82 1.81 1.35 2.04
FCHO1 ENST00000594202 51.85 10.45 29.29 0.61 2.23 0.84 1.81 0.50 1.34
PLOD3 ENST00000223127 51.85 42.59 45.91 0.61 0.59 0.70 1.81 1.89 1.98
HIGD2A ENST00000274787 51.86 81.23 68.52 0.61 0.34 0.47 1.81 0.55 1.06
PCDHGB7 ENST00000398594 51.86 38.13 43.33 0.61 0.77 0.63 1.81 1.71 2.00
DNAH3 ENST00000261383 51.87 42.95 46.11 0.61 0.63 0.67 1.81 1.90 1.96
PEX11A ENST00000300056 51.87 78.11 66.71 0.61 0.43 0.54 1.81 0.74 1.20
OR13C4 ENST00000277216 51.88 95.75 76.94 0.61 0.23 0.37 1.81 0.20 0.61
ASB17 ENST00000284142 51.88 80.42 68.13 0.61 0.37 0.49 1.80 0.59 1.08
SLC12A3 ENST00000438926 51.89 65.63 58.89 0.61 0.53 0.49 1.80 1.21 1.65
ESR2 ENST00000341099 51.89 54.47 52.49 0.61 0.59 0.61 1.80 1.66 1.91
PRSS23 ENST00000280258 51.90 57.92 54.47 0.61 0.57 0.57 1.80 1.46 1.76
OR52H1 ENST00000322653 51.90 78.90 67.16 0.61 0.40 0.52 1.80 0.70 1.17
ZNF212 ENST00000335870 51.91 53.94 52.15 0.61 0.65 0.61 1.80 1.70 1.90

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