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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
ANXA11 ENST00000438331 70.25 55.44 64.11 0.49 0.58 0.52 0.91 1.60 1.37
PHLDA2 ENST00000314222 70.25 86.88 81.95 0.49 0.22 0.37 0.92 0.41 0.47
CD69 ENST00000228434 70.26 48.42 59.67 0.49 0.63 0.49 0.92 2.02 1.67
CLDN17 ENST00000286808 70.26 90.68 83.84 0.49 0.25 0.34 0.92 0.36 0.42
SEC16B ENST00000308284 70.27 53.03 62.56 0.49 0.66 0.48 0.92 1.77 1.40
MPST ENST00000397129 70.28 74.72 75.44 0.49 0.54 0.37 0.92 0.96 0.66
GPAT2 ENST00000434632 70.28 66.13 70.51 0.49 0.53 0.43 0.92 1.20 0.91
UGT1A10 ENST00000344644 70.29 87.77 82.42 0.49 0.24 0.33 0.92 0.37 0.44
CRB2 ENST00000373631 70.29 48.16 59.53 0.49 0.63 0.49 0.92 1.97 1.69
PNMA2 ENST00000522362 70.30 62.61 68.45 0.49 0.51 0.47 0.92 1.31 1.06
BTBD16 ENST00000260723 70.30 70.81 73.35 0.49 0.49 0.43 0.92 1.08 0.78
TRMT2A ENST00000252136 70.31 47.02 58.78 0.49 0.68 0.51 0.92 1.98 1.64
MPDZ ENST00000541718 70.31 48.62 59.87 0.49 0.63 0.49 0.92 2.00 1.63
SKA3 ENST00000314759 70.32 56.02 64.46 0.49 0.49 0.51 0.92 1.56 1.34
TAF1L ENST00000242310 70.32 13.95 40.41 0.49 2.05 0.80 0.92 0.60 2.02
MROH7 ENST00000421030 70.33 54.48 63.59 0.49 0.59 0.49 0.92 1.66 1.40
PADI4 ENST00000375448 70.33 64.22 69.43 0.49 0.49 0.43 0.92 1.20 0.98
FOPNL ENST00000255759 70.34 84.63 80.78 0.49 0.27 0.39 0.92 0.42 0.52
PPAPDC1B ENST00000424479 70.34 94.55 85.77 0.49 0.23 0.33 0.92 0.24 0.33
TNIP3 ENST00000509841 70.35 28.67 48.37 0.49 1.18 0.67 0.92 1.29 1.88
GPR182 ENST00000300098 70.35 75.32 75.84 0.49 0.49 0.38 0.92 0.90 0.63
NINJ2 ENST00000305108 70.36 79.96 78.41 0.49 0.37 0.38 0.92 0.61 0.54
SPATA5L1 ENST00000305560 70.36 58.28 65.95 0.49 0.54 0.51 0.92 1.43 1.24
ELP5 ENST00000396628 70.37 88.84 82.95 0.49 0.25 0.32 0.91 0.35 0.40
PRODH2 ENST00000301175 70.37 68.06 71.76 0.49 0.52 0.46 0.91 1.19 0.81

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