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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
RNF123 ENST00000327697 26.99 21.99 22.65 1.29 1.48 1.18 1.37 0.81 0.97
DDHD1 ENST00000323669 27.00 13.67 18.27 1.29 2.06 1.66 1.37 0.59 0.79
RPS11 ENST00000270625 27.00 16.78 19.93 1.28 1.68 1.46 1.37 0.71 0.84
RXFP2 ENST00000298386 27.01 56.05 39.87 1.28 0.49 0.78 1.37 1.55 2.02
LRFN2 ENST00000338305 27.01 39.36 31.41 1.28 0.70 0.87 1.37 1.65 1.55
LNX2 ENST00000316334 27.02 34.43 28.86 1.28 0.80 0.82 1.37 1.56 1.31
ZNF330 ENST00000262990 27.02 29.57 26.39 1.28 1.10 1.01 1.37 1.39 1.25
HCN2 ENST00000251287 27.03 17.89 20.58 1.28 1.52 1.48 1.37 0.73 0.88
EXTL2 ENST00000370114 27.03 56.99 40.27 1.28 0.56 0.80 1.37 1.53 1.99
EXOC2 ENST00000230449 27.04 30.76 27.06 1.28 1.06 0.99 1.37 1.37 1.27
CCDC149 ENST00000504487 27.04 43.01 33.19 1.28 0.61 0.87 1.37 1.89 1.69
NAA20 ENST00000334982 27.05 57.52 40.51 1.28 0.56 0.80 1.36 1.48 2.04
SALL2 ENST00000327430 27.05 37.34 30.40 1.27 0.76 0.81 1.36 1.65 1.46
POU6F2 ENST00000403058 27.06 25.88 24.53 1.27 1.21 1.08 1.36 1.08 1.08
DIXDC1 ENST00000440460 27.06 39.03 31.25 1.27 0.70 0.86 1.36 1.64 1.56
MAST2 ENST00000361297 27.07 38.60 31.03 1.27 0.73 0.82 1.37 1.66 1.51
SOSTDC1 ENST00000307068 27.08 55.36 39.55 1.27 0.57 0.80 1.37 1.61 2.03
CDC6 ENST00000209728 27.08 56.06 39.92 1.27 0.49 0.81 1.37 1.55 2.01
TLL1 ENST00000061240 27.09 16.19 19.65 1.27 1.81 1.53 1.37 0.70 0.85
ONECUT2 ENST00000491143 27.09 18.09 20.72 1.27 1.53 1.47 1.37 0.74 0.88
IFT80 ENST00000326448 27.10 53.74 38.67 1.27 0.63 0.82 1.37 1.70 2.02
STRA8 ENST00000275764 27.10 44.41 33.91 1.27 0.61 0.90 1.37 1.97 1.73
CDC26 ENST00000374206 27.11 46.53 34.99 1.25 0.73 0.89 1.37 2.02 1.73
RP2 ENST00000218340 27.11 12.43 17.69 1.25 2.06 1.68 1.37 0.59 0.78
RECK ENST00000377966 27.12 35.82 29.66 1.25 0.80 0.85 1.38 1.58 1.39

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