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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
OR10A6 ENST00000309838 76.19 92.84 87.67 0.34 0.29 0.24 0.76 0.30 0.31
SHBG ENST00000380450 76.19 59.07 69.84 0.34 0.49 0.46 0.76 1.44 0.93
OR1J4 ENST00000340750 76.20 76.22 79.47 0.34 0.43 0.38 0.76 0.85 0.52
ACD ENST00000393919 76.20 68.98 75.56 0.34 0.54 0.37 0.76 1.15 0.64
LURAP1L ENST00000319264 76.21 74.54 78.63 0.34 0.53 0.39 0.76 1.00 0.55
GUK1 ENST00000366728 76.22 76.65 79.73 0.34 0.40 0.38 0.76 0.83 0.53
CLEC12B ENST00000338896 76.22 61.42 71.28 0.34 0.54 0.43 0.76 1.40 0.87
GPATCH4 ENST00000438976 76.23 71.79 77.16 0.34 0.51 0.35 0.75 1.07 0.59
EP400NL ENST00000443539 76.23 79.53 81.22 0.34 0.38 0.38 0.74 0.66 0.49
LYSMD4 ENST00000344791 76.24 75.22 79.05 0.34 0.49 0.39 0.74 0.90 0.53
OR5P2 ENST00000329434 76.24 82.76 82.87 0.34 0.33 0.32 0.74 0.50 0.41
TOR2A ENST00000373284 76.25 43.42 60.31 0.34 0.61 0.47 0.74 1.95 1.60
GHDC ENST00000301671 76.25 54.85 67.36 0.34 0.57 0.52 0.74 1.63 1.15
SMIM3 ENST00000526627 76.26 97.30 89.87 0.34 0.23 0.18 0.74 0.19 0.23
IL24 ENST00000391929 76.26 83.47 83.24 0.34 0.27 0.29 0.74 0.47 0.40
ZNF432 ENST00000594154 76.27 62.73 72.14 0.34 0.51 0.43 0.74 1.31 0.82
TTF1 ENST00000334270 76.27 50.37 64.69 0.34 0.66 0.51 0.74 1.95 1.33
HN1L ENST00000248098 76.28 45.16 61.37 0.34 0.70 0.44 0.74 1.98 1.48
KREMEN2 ENST00000303746 76.28 46.85 62.40 0.34 0.71 0.48 0.74 1.97 1.41
CSTB ENST00000291568 76.29 91.28 86.97 0.34 0.23 0.28 0.74 0.34 0.30
NUDT8 ENST00000376693 76.29 89.96 86.33 0.34 0.25 0.33 0.74 0.37 0.33
CXCL1 ENST00000395761 76.30 62.66 72.09 0.34 0.51 0.43 0.74 1.31 0.81
COL26A1 ENST00000313669 76.30 40.46 58.45 0.34 0.62 0.52 0.74 1.77 1.65
TMEM207 ENST00000354905 76.31 95.43 88.99 0.34 0.24 0.19 0.74 0.20 0.27
PRDX5 ENST00000265462 76.31 74.36 78.62 0.34 0.53 0.38 0.74 1.00 0.55

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