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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
UGT1A1 ENST00000609767 71.15 73.33 75.16 0.42 0.54 0.38 0.86 1.02 0.67
SERPINB10 ENST00000238508 71.16 79.55 78.59 0.42 0.38 0.38 0.86 0.66 0.54
OR2B6 ENST00000244623 71.16 64.46 70.02 0.42 0.48 0.47 0.86 1.22 0.91
SCAMP4 ENST00000316097 71.17 45.64 58.47 0.42 0.73 0.51 0.86 2.01 1.65
TMEM223 ENST00000307366 71.17 89.61 83.78 0.42 0.27 0.34 0.86 0.37 0.41
OR10J5 ENST00000334857 71.18 72.08 74.56 0.42 0.52 0.40 0.86 1.04 0.69
FAM71E1 ENST00000595790 71.18 82.03 79.91 0.42 0.34 0.37 0.86 0.50 0.52
PIANP ENST00000540656 71.19 31.71 50.46 0.42 0.95 0.67 0.86 1.46 1.88
WDR87 ENST00000303868 71.19 52.19 62.62 0.42 0.62 0.48 0.86 1.84 1.40
PTTG1IP ENST00000330938 71.20 50.19 61.37 0.42 0.67 0.44 0.86 1.99 1.48
ABCG8 ENST00000272286 71.20 74.86 76.04 0.42 0.53 0.38 0.86 0.95 0.62
CHIT1 ENST00000367229 71.21 72.84 74.96 0.42 0.49 0.40 0.86 1.05 0.65
C8A ENST00000361249 71.22 64.56 70.12 0.42 0.48 0.46 0.86 1.22 0.90
SMN1 ENST00000380707 71.22 93.19 85.57 0.42 0.28 0.32 0.86 0.30 0.35
ZNHIT6 ENST00000370574 71.23 64.10 69.90 0.42 0.49 0.46 0.86 1.20 0.92
NKX6-2 ENST00000368592 71.23 71.78 74.38 0.42 0.51 0.40 0.86 1.07 0.70
NCR3 ENST00000340027 71.24 81.23 79.50 0.42 0.34 0.38 0.86 0.55 0.52
N4BP3 ENST00000274605 71.24 42.94 56.93 0.42 0.63 0.49 0.86 1.90 1.71
CYP3A4 ENST00000336411 71.25 62.42 68.85 0.42 0.52 0.46 0.86 1.32 1.05
BAIAP3 ENST00000324385 71.25 52.67 63.02 0.42 0.68 0.51 0.86 1.80 1.39
OR10T2 ENST00000334438 71.26 67.11 71.74 0.40 0.54 0.46 0.86 1.23 0.81
CBR4 ENST00000306193 71.26 88.03 83.00 0.40 0.25 0.32 0.86 0.38 0.40
ABCB5 ENST00000404938 71.27 61.27 68.26 0.40 0.53 0.52 0.85 1.39 1.08
WBSCR16 ENST00000329959 71.27 50.18 61.40 0.40 0.67 0.44 0.85 1.99 1.48
KLHDC1 ENST00000359332 71.28 51.14 61.96 0.40 0.66 0.48 0.85 1.91 1.46

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