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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
SPINK2 ENST00000248701 88.71 64.90 80.14 0.19 0.48 0.35 0.33 1.25 0.53
ZNF525 ENST00000474037 88.72 76.62 85.94 0.19 0.42 0.33 0.33 0.83 0.33
GCNT7 ENST00000243913 88.72 51.17 72.64 0.19 0.66 0.46 0.33 1.91 0.81
OR11H12 ENST00000550708 88.73 97.57 95.89 0.19 0.22 0.07 0.33 0.20 0.11
CCDC168 ENST00000322527 88.74 34.84 62.72 0.19 0.76 0.49 0.33 1.55 1.39
ZNF80 ENST00000482457 88.74 99.35 96.27 0.19 0.16 0.07 0.33 0.12 0.09
POTEJ ENST00000409602 88.75 71.50 83.49 0.19 0.53 0.33 0.33 1.06 0.40
DDX53 ENST00000327968 88.75 43.42 68.03 0.19 0.61 0.51 0.33 1.95 1.10
IL9R ENST00000244174 88.76 95.85 95.05 0.19 0.22 0.09 0.33 0.20 0.10
DPPA4 ENST00000335658 88.76 46.93 70.09 0.19 0.71 0.46 0.33 1.94 0.91
STARD9 ENST00000290607 88.77 32.87 61.51 0.19 0.84 0.46 0.33 1.44 1.48
TMEM123 ENST00000398136 88.77 33.20 61.70 0.19 0.82 0.46 0.33 1.50 1.46
OR11H1 ENST00000252835 88.78 96.93 95.63 0.19 0.24 0.08 0.33 0.19 0.11
ZNF66 ENST00000344519 88.78 80.36 87.72 0.19 0.37 0.24 0.33 0.59 0.32
ADM2 ENST00000395738 88.79 80.78 87.92 0.19 0.37 0.24 0.33 0.57 0.32
TMEM133 ENST00000303130 88.79 98.26 96.35 0.19 0.21 0.07 0.33 0.15 0.09
OR13G1 ENST00000359688 88.80 86.67 90.80 0.19 0.24 0.15 0.33 0.40 0.20
SERHL2 ENST00000327678 88.80 96.96 95.65 0.19 0.24 0.08 0.33 0.19 0.11
LY9 ENST00000263285 88.81 61.37 78.34 0.19 0.54 0.38 0.33 1.40 0.54
OR2M5 ENST00000366476 88.81 98.18 96.30 0.19 0.20 0.07 0.33 0.16 0.09
OLAH ENST00000378217 88.82 80.20 87.66 0.19 0.37 0.25 0.33 0.59 0.31
KRTAP19-3 ENST00000334063 88.82 99.20 96.89 0.19 0.15 0.08 0.33 0.13 0.07
ZNF549 ENST00000376233 88.83 85.25 90.10 0.19 0.25 0.18 0.33 0.46 0.22
TRIM61 ENST00000329314 88.83 89.68 91.99 0.19 0.27 0.14 0.33 0.36 0.16
LIME1 ENST00000309546 88.84 75.19 85.36 0.19 0.49 0.34 0.33 0.91 0.35

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