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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
PIGQ ENST00000026218 71.93 46.19 59.28 0.33 0.73 0.51 0.81 2.03 1.68
BANK1 ENST00000322953 71.93 46.24 59.34 0.33 0.73 0.51 0.81 2.03 1.69
CARKD ENST00000309957 71.94 43.32 57.61 0.33 0.59 0.51 0.81 1.94 1.68
TNFRSF1B ENST00000376259 71.94 19.28 44.05 0.33 1.47 0.61 0.81 0.76 2.02
LGALS4 ENST00000307751 71.95 63.36 69.89 0.33 0.48 0.46 0.81 1.30 0.92
BEX1 ENST00000372728 71.95 64.19 70.38 0.33 0.49 0.43 0.81 1.22 0.91
HOXB2 ENST00000330070 71.96 74.92 76.52 0.33 0.53 0.38 0.81 0.94 0.61
C9orf89 ENST00000375464 71.96 79.58 79.09 0.33 0.38 0.39 0.81 0.66 0.53
SCRIB ENST00000356994 71.97 12.01 40.25 0.33 2.07 0.81 0.81 0.57 2.00
PGLYRP4 ENST00000359650 71.97 89.60 84.05 0.33 0.27 0.35 0.81 0.37 0.42
ZNF585B ENST00000532828 71.98 43.60 57.78 0.34 0.62 0.51 0.81 1.95 1.67
A2ML1 ENST00000299698 71.98 52.10 63.13 0.34 0.61 0.49 0.81 1.85 1.39
DENND1C ENST00000381480 71.99 35.19 52.97 0.34 0.76 0.61 0.81 1.58 1.87
CPA3 ENST00000296046 72.00 73.23 75.58 0.34 0.54 0.38 0.81 1.02 0.64
KRT37 ENST00000225550 72.00 73.84 75.93 0.34 0.53 0.38 0.81 1.03 0.62
OR1L3 ENST00000304820 72.01 94.42 86.44 0.34 0.23 0.30 0.81 0.24 0.32
COQ2 ENST00000311469 72.01 48.45 60.81 0.34 0.63 0.43 0.81 2.02 1.60
ASTL ENST00000342380 72.02 63.41 69.93 0.34 0.48 0.47 0.81 1.28 0.92
GSG1L ENST00000447459 72.02 24.29 46.87 0.34 1.30 0.68 0.81 0.99 1.88
C3orf20 ENST00000253697 72.03 63.80 70.15 0.34 0.49 0.44 0.81 1.22 0.90
OR51S1 ENST00000322101 72.03 80.72 79.64 0.34 0.37 0.38 0.81 0.57 0.53
TLDC2 ENST00000217320 72.04 46.38 59.48 0.34 0.73 0.49 0.81 2.04 1.70
MIXL1 ENST00000366810 72.04 82.52 80.60 0.34 0.34 0.39 0.81 0.52 0.52
AAED1 ENST00000375234 72.05 90.41 84.58 0.34 0.25 0.34 0.80 0.37 0.40
HYDIN ENST00000393567 72.05 22.55 46.02 0.34 1.48 0.68 0.81 0.84 1.96

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