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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
TRIM4 ENST00000355947 81.10 73.65 80.69 0.33 0.52 0.39 0.60 1.03 0.52
IMP3 ENST00000314852 81.10 97.24 91.93 0.33 0.23 0.14 0.60 0.19 0.17
RAB11FIP1 ENST00000330843 81.11 46.35 65.19 0.33 0.73 0.53 0.60 2.04 1.30
NUBP2 ENST00000262302 81.11 66.31 76.85 0.33 0.54 0.35 0.60 1.20 0.61
NPDC1 ENST00000371601 81.12 32.65 56.70 0.33 0.85 0.52 0.60 1.46 1.71
TMEM258 ENST00000537328 81.12 90.81 89.09 0.33 0.25 0.19 0.60 0.35 0.26
DERA ENST00000428559 81.13 50.87 67.89 0.33 0.63 0.51 0.59 1.92 1.11
ZNF891 ENST00000537226 81.13 63.76 75.36 0.33 0.49 0.37 0.59 1.22 0.66
RCSD1 ENST00000367854 81.14 33.73 57.35 0.33 0.84 0.51 0.59 1.56 1.67
FAM194A ENST00000295910 81.14 78.78 83.32 0.33 0.42 0.32 0.59 0.71 0.40
AMER3 ENST00000423981 81.15 30.49 55.49 0.33 1.09 0.51 0.59 1.37 1.73
ACR ENST00000216139 81.15 40.35 61.44 0.33 0.61 0.44 0.59 1.75 1.47
SPATA6L ENST00000475086 81.16 87.98 87.71 0.33 0.25 0.24 0.59 0.37 0.32
LRRC45 ENST00000306688 81.16 43.44 63.49 0.33 0.61 0.49 0.59 1.95 1.39
RIBC2 ENST00000538017 81.17 80.74 84.23 0.33 0.37 0.34 0.59 0.57 0.42
TEPP ENST00000290871 81.17 53.82 69.72 0.33 0.63 0.44 0.59 1.71 0.94
PNPLA4 ENST00000381042 81.18 70.06 78.87 0.33 0.53 0.39 0.59 1.14 0.52
MTHFSD ENST00000360900 81.18 83.62 85.72 0.33 0.27 0.33 0.60 0.47 0.33
VWDE ENST00000275358 81.19 61.45 74.17 0.33 0.54 0.39 0.60 1.40 0.69
SWI5 ENST00000320188 81.19 63.91 75.49 0.33 0.48 0.38 0.60 1.22 0.66
GSTA2 ENST00000493422 81.20 85.48 86.53 0.33 0.25 0.30 0.60 0.45 0.33
CYP4F3 ENST00000221307 81.20 73.76 80.78 0.33 0.52 0.39 0.60 1.03 0.52
TCERG1L ENST00000368642 81.21 53.48 69.51 0.33 0.65 0.44 0.60 1.72 0.96
TDRP ENST00000523656 81.21 93.17 90.24 0.33 0.28 0.16 0.60 0.30 0.22
TREML2 ENST00000483722 81.22 83.81 85.83 0.33 0.27 0.33 0.60 0.47 0.33

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