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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
FANCM ENST00000267430 54.63 30.36 40.65 0.63 1.08 0.81 1.71 1.40 2.05
DNTT ENST00000371174 54.63 54.96 54.36 0.63 0.57 0.59 1.72 1.64 1.75
JAGN1 ENST00000307768 54.64 72.41 64.97 0.63 0.51 0.51 1.72 1.03 1.32
CPA2 ENST00000222481 54.64 74.76 66.42 0.63 0.54 0.52 1.72 0.96 1.21
ARHGAP22 ENST00000417912 54.65 47.51 50.07 0.63 0.62 0.62 1.72 2.01 1.92
MT2A ENST00000245185 54.65 96.52 78.82 0.63 0.22 0.39 1.72 0.19 0.52
ZWILCH ENST00000307897 54.66 55.42 54.61 0.63 0.58 0.56 1.72 1.60 1.74
LRCH3 ENST00000334859 54.66 42.64 47.41 0.63 0.59 0.65 1.72 1.90 1.87
PIPOX ENST00000323372 54.67 69.52 63.19 0.63 0.54 0.49 1.72 1.11 1.36
SAMD9 ENST00000379958 54.67 69.10 62.87 0.63 0.56 0.51 1.72 1.14 1.40
PSMB10 ENST00000358514 54.68 77.23 67.87 0.63 0.43 0.51 1.72 0.78 1.12
TK2 ENST00000451102 54.68 63.84 59.57 0.63 0.49 0.49 1.72 1.21 1.69
ADRB3 ENST00000345060 54.69 85.32 72.68 0.63 0.25 0.43 1.72 0.45 0.81
GORAB ENST00000367763 54.69 53.02 53.30 0.63 0.66 0.62 1.72 1.77 1.85
RRAGB ENST00000262850 54.70 22.55 36.81 0.63 1.48 0.82 1.72 0.84 1.94
PIR ENST00000380421 54.70 87.56 73.91 0.63 0.23 0.40 1.72 0.37 0.70
TIGD6 ENST00000296736 54.71 68.93 62.77 0.63 0.54 0.48 1.72 1.17 1.39
TGFA ENST00000295400 54.71 27.91 39.67 0.63 1.19 0.80 1.73 1.19 2.04
CCKAR ENST00000295589 54.72 48.45 50.62 0.63 0.63 0.66 1.73 2.02 1.85
KCTD11 ENST00000333751 54.72 81.26 70.26 0.63 0.34 0.43 1.73 0.54 0.91
SERPINA11 ENST00000334708 54.73 82.56 71.06 0.63 0.34 0.43 1.73 0.51 0.86
FAM175A ENST00000321945 54.73 58.32 56.30 0.63 0.54 0.49 1.73 1.42 1.75
ENPP3 ENST00000414305 54.74 57.06 55.59 0.63 0.56 0.53 1.73 1.52 1.75
DPT ENST00000367817 54.74 65.99 60.98 0.63 0.56 0.43 1.73 1.22 1.58
AP3S2 ENST00000336418 54.75 77.25 67.89 0.63 0.42 0.51 1.72 0.78 1.11

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