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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
FCHO2 ENST00000430046 69.22 7.96 36.77 0.56 2.54 0.82 0.98 0.44 1.94
TRIM14 ENST00000341469 69.22 36.29 51.95 0.56 0.82 0.62 0.98 1.61 1.92
MAN1B1 ENST00000371589 69.23 44.28 56.57 0.56 0.61 0.52 0.98 1.95 1.70
BDKRB1 ENST00000216629 69.23 61.91 67.37 0.56 0.56 0.52 0.97 1.35 1.15
ZNF772 ENST00000343280 69.24 49.23 59.54 0.56 0.66 0.49 0.97 2.02 1.69
IFT74 ENST00000443698 69.24 44.03 56.45 0.54 0.61 0.52 0.98 1.97 1.70
THAP10 ENST00000249861 69.25 61.55 67.17 0.54 0.54 0.52 0.98 1.41 1.17
ABCC6 ENST00000205557 69.25 56.54 64.17 0.54 0.52 0.51 0.98 1.54 1.36
IL5 ENST00000231454 69.26 76.83 76.09 0.54 0.42 0.38 0.98 0.81 0.62
MEIS3 ENST00000561293 69.26 49.64 59.84 0.54 0.66 0.49 0.98 2.02 1.63
ZNF75D ENST00000370766 69.27 54.68 63.01 0.54 0.58 0.51 0.98 1.65 1.39
OR4F15 ENST00000332238 69.27 72.31 73.58 0.54 0.51 0.40 0.98 1.03 0.74
NUDT16L1 ENST00000304301 69.28 86.89 81.43 0.53 0.22 0.35 0.98 0.41 0.48
C9orf9 ENST00000350499 69.28 85.18 80.56 0.53 0.25 0.39 0.98 0.45 0.51
C12orf39 ENST00000256969 69.29 74.91 75.03 0.53 0.53 0.39 0.98 0.94 0.66
KIAA0754 ENST00000530275 69.29 30.04 48.56 0.53 1.09 0.68 0.98 1.43 1.85
MEOX1 ENST00000318579 69.30 69.66 72.10 0.53 0.53 0.43 0.98 1.12 0.81
NMU ENST00000264218 69.30 47.90 58.71 0.53 0.59 0.52 0.98 1.99 1.65
SPSB2 ENST00000524270 69.31 55.25 63.45 0.53 0.57 0.51 0.98 1.62 1.38
LRRIQ4 ENST00000340806 69.31 61.90 67.41 0.53 0.56 0.52 0.98 1.35 1.15
BCAT1 ENST00000539282 69.32 57.58 64.86 0.53 0.57 0.51 0.98 1.48 1.34
CD70 ENST00000245903 69.32 86.96 81.49 0.53 0.22 0.35 0.98 0.40 0.48
IL36RN ENST00000393200 69.33 92.71 84.33 0.53 0.29 0.33 0.98 0.30 0.40
TMEM175 ENST00000264771 69.34 59.94 66.33 0.53 0.53 0.53 0.98 1.36 1.20
SERINC2 ENST00000373710 69.34 68.80 71.61 0.53 0.53 0.44 0.98 1.19 0.83

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