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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
GPR179 ENST00000342292 68.03 45.98 56.86 0.58 0.77 0.52 1.03 2.02 1.70
SH2B2 ENST00000536178 68.65 49.22 59.11 0.56 0.66 0.49 0.94 2.02 1.68
ZNF772 ENST00000343280 69.24 49.23 59.54 0.56 0.66 0.49 0.97 2.02 1.69
MEIS3 ENST00000561293 69.26 49.64 59.84 0.54 0.66 0.49 0.98 2.02 1.63
ADCK2 ENST00000072869 69.61 49.74 60.11 0.54 0.66 0.48 0.97 2.02 1.61
IAH1 ENST00000497473 70.22 49.74 60.51 0.49 0.66 0.44 0.91 2.02 1.58
CD69 ENST00000228434 70.26 48.42 59.67 0.49 0.63 0.49 0.92 2.02 1.67
RPLP2 ENST00000321153 70.63 49.70 60.74 0.49 0.66 0.44 0.91 2.02 1.61
FAM71F2 ENST00000480462 70.87 48.81 60.30 0.47 0.63 0.47 0.87 2.02 1.59
COQ2 ENST00000311469 72.01 48.45 60.81 0.34 0.63 0.43 0.81 2.02 1.60
MLF1IP ENST00000281453 72.80 49.25 61.76 0.32 0.66 0.46 0.78 2.02 1.47
KDM8 ENST00000441782 73.51 45.94 60.16 0.34 0.76 0.48 0.78 2.02 1.61
HLA-B ENST00000412585 74.07 45.88 60.48 0.35 0.75 0.44 0.82 2.02 1.58
LINS ENST00000314742 74.09 49.63 62.82 0.35 0.66 0.48 0.81 2.02 1.39
CASP1 ENST00000533400 75.24 46.45 61.56 0.38 0.73 0.46 0.76 2.02 1.48
PLEKHA4 ENST00000263265 76.00 46.01 61.74 0.34 0.77 0.46 0.76 2.02 1.46
CAGE1 ENST00000502583 76.32 49.59 64.24 0.34 0.66 0.51 0.74 2.02 1.35
FCRL1 ENST00000368176 79.65 49.28 66.13 0.33 0.65 0.52 0.57 2.02 1.21
USP40 ENST00000450966 79.99 45.82 64.15 0.32 0.75 0.51 0.58 2.02 1.37
HS3ST6 ENST00000443547 80.06 48.80 66.09 0.32 0.63 0.51 0.59 2.02 1.22
MTL5 ENST00000255087 81.94 45.75 65.38 0.32 0.75 0.53 0.57 2.02 1.32
CCDC40 ENST00000397545 83.09 45.71 66.04 0.29 0.75 0.51 0.55 2.02 1.22
ZNF720 ENST00000316491 83.93 49.22 68.58 0.29 0.66 0.47 0.48 2.02 1.05
TPTE2 ENST00000400230 86.79 48.47 69.86 0.24 0.63 0.46 0.40 2.02 0.92
CD80 ENST00000264246 87.17 49.81 70.81 0.23 0.66 0.43 0.38 2.02 0.87

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