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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
KRT82 ENST00000257974 69.99 82.68 79.58 0.51 0.34 0.38 0.93 0.50 0.52
TTLL3 ENST00000426895 70.00 67.22 71.01 0.51 0.54 0.43 0.93 1.22 0.85
LRGUK ENST00000285928 70.00 51.30 61.32 0.51 0.65 0.44 0.93 1.90 1.48
OR2C1 ENST00000304936 70.01 85.33 81.02 0.49 0.25 0.39 0.93 0.45 0.50
AMY2B ENST00000361355 70.01 89.05 82.90 0.49 0.27 0.32 0.93 0.35 0.40
ZNF34 ENST00000343459 70.02 38.15 53.48 0.49 0.77 0.63 0.93 1.72 1.82
SLC12A7 ENST00000264930 70.02 46.94 58.56 0.49 0.71 0.51 0.93 1.94 1.65
GAL3ST3 ENST00000312006 70.03 89.69 83.23 0.49 0.27 0.29 0.93 0.37 0.40
IL22RA1 ENST00000270800 70.03 32.07 50.04 0.49 0.91 0.61 0.93 1.47 1.92
WDR49 ENST00000308378 70.04 68.83 72.05 0.49 0.53 0.43 0.93 1.19 0.81
EMR1 ENST00000312053 70.04 60.57 67.03 0.49 0.52 0.52 0.93 1.41 1.17
GSTP1 ENST00000398606 70.05 39.54 54.34 0.49 0.68 0.59 0.94 1.63 1.73
PYROXD2 ENST00000370575 70.05 66.29 70.49 0.49 0.54 0.43 0.94 1.20 0.91
MS4A15 ENST00000405633 70.06 76.08 76.11 0.49 0.43 0.38 0.94 0.86 0.62
ODF3 ENST00000325113 70.06 34.65 51.50 0.49 0.80 0.63 0.94 1.53 1.91
CENPN ENST00000393335 70.07 33.15 50.67 0.49 0.82 0.66 0.94 1.51 1.85
VAMP7 ENST00000262640 70.07 45.57 57.84 0.49 0.75 0.51 0.93 1.98 1.66
MEDAG ENST00000380482 70.08 72.27 73.96 0.49 0.51 0.40 0.94 1.03 0.69
CARD6 ENST00000254691 70.08 69.38 72.43 0.49 0.56 0.44 0.94 1.14 0.83
CLYBL ENST00000376360 70.09 74.05 75.00 0.49 0.53 0.39 0.94 1.03 0.66
C9orf24 ENST00000297623 70.09 60.83 67.23 0.49 0.56 0.52 0.94 1.41 1.16
EFHD1 ENST00000264059 70.10 79.59 78.04 0.49 0.38 0.39 0.94 0.66 0.54
AGA ENST00000264595 70.10 56.30 64.50 0.49 0.52 0.51 0.94 1.55 1.34
CLEC18B ENST00000339953 70.11 55.05 63.86 0.49 0.58 0.49 0.93 1.63 1.39
AGMO ENST00000342526 70.12 86.39 81.63 0.49 0.25 0.37 0.93 0.42 0.47

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