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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
TRAPPC6A ENST00000006275 78.77 94.41 89.70 0.35 0.23 0.18 0.65 0.24 0.23
OR2AE1 ENST00000316368 78.78 87.85 86.51 0.35 0.24 0.30 0.65 0.38 0.33
SCLY ENST00000254663 78.78 64.07 74.29 0.35 0.49 0.39 0.65 1.21 0.70
ATHL1 ENST00000409548 78.79 55.76 69.44 0.35 0.52 0.43 0.65 1.58 0.98
CDKN2AIPNL ENST00000458198 78.79 58.92 71.34 0.35 0.53 0.43 0.64 1.42 0.87
AKR7A3 ENST00000361640 78.80 95.60 90.24 0.35 0.23 0.16 0.65 0.21 0.22
USP36 ENST00000542802 78.80 27.21 52.25 0.35 1.25 0.59 0.65 1.15 1.89
KLRB1 ENST00000229402 78.81 76.24 80.83 0.35 0.43 0.39 0.65 0.85 0.51
MT1A ENST00000290705 78.81 93.91 89.48 0.35 0.25 0.18 0.64 0.26 0.24
PNLIPRP2 ENST00000537242 78.82 68.81 76.95 0.35 0.53 0.37 0.64 1.19 0.61
BCAM ENST00000270233 78.82 42.24 61.13 0.35 0.61 0.43 0.64 1.89 1.51
CATSPERB ENST00000256343 78.83 47.73 64.61 0.34 0.59 0.51 0.64 1.99 1.32
AMN ENST00000299155 78.83 43.33 61.83 0.34 0.59 0.47 0.64 1.94 1.46
C9orf171 ENST00000343036 78.84 70.61 77.91 0.34 0.51 0.38 0.65 1.08 0.54
NAT1 ENST00000545197 78.84 93.54 89.30 0.33 0.28 0.19 0.65 0.28 0.25
FAM21C ENST00000374362 78.85 45.71 63.47 0.33 0.75 0.49 0.65 2.02 1.38
KIFC2 ENST00000301332 78.85 44.74 62.74 0.33 0.66 0.48 0.65 1.98 1.39
FAM26F ENST00000368605 78.86 89.42 87.36 0.33 0.27 0.28 0.65 0.37 0.31
OR13A1 ENST00000553795 78.86 81.24 83.40 0.33 0.34 0.33 0.65 0.54 0.40
LGALS2 ENST00000215886 78.87 79.71 82.70 0.33 0.37 0.32 0.65 0.64 0.42
OR5D14 ENST00000335605 78.88 95.95 90.47 0.33 0.22 0.14 0.65 0.20 0.21
HOXB7 ENST00000239165 78.88 80.10 82.87 0.33 0.37 0.32 0.65 0.60 0.41
ERVFRD-1 ENST00000472091 78.89 75.65 80.59 0.32 0.44 0.39 0.65 0.90 0.52
C15orf60 ENST00000331090 78.89 59.91 72.00 0.32 0.53 0.42 0.65 1.36 0.81
CBFA2T3 ENST00000268679 78.90 24.70 50.85 0.32 1.29 0.67 0.65 1.05 1.84

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