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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
MGST2 ENST00000265498 61.08 52.65 56.69 0.61 0.68 0.52 1.32 1.81 1.71
KRT27 ENST00000301656 61.09 62.51 62.73 0.61 0.53 0.48 1.32 1.31 1.39
NRDE2 ENST00000354366 61.09 41.25 50.18 0.61 0.61 0.63 1.32 1.83 1.90
PDCD7 ENST00000204549 61.10 61.66 62.20 0.61 0.56 0.48 1.32 1.39 1.45
PDZRN4 ENST00000402685 61.10 29.58 43.69 0.62 1.10 0.61 1.32 1.39 2.01
THRSP ENST00000281030 61.11 85.36 76.32 0.62 0.25 0.35 1.32 0.45 0.61
ZNF311 ENST00000377179 61.11 46.54 53.26 0.62 0.75 0.61 1.33 2.02 1.87
PMM2 ENST00000268261 61.12 92.63 80.22 0.62 0.29 0.37 1.32 0.31 0.52
ULK4 ENST00000301831 61.12 59.51 60.93 0.62 0.51 0.43 1.32 1.41 1.57
OR52W1 ENST00000311352 61.13 86.65 77.04 0.62 0.24 0.37 1.32 0.40 0.61
C17orf62 ENST00000437807 61.13 73.79 69.68 0.62 0.53 0.44 1.32 1.02 0.95
TMX1 ENST00000457354 61.14 39.68 49.29 0.62 0.66 0.70 1.32 1.66 1.85
ZNF2 ENST00000340539 61.14 32.66 45.61 0.62 0.85 0.68 1.32 1.46 1.99
PINK1 ENST00000321556 61.15 65.26 64.55 0.62 0.51 0.51 1.32 1.24 1.33
OR2V1 ENST00000329365 61.15 93.86 80.82 0.62 0.25 0.39 1.32 0.26 0.51
DNAJA3 ENST00000262375 61.16 27.78 42.79 0.62 1.24 0.70 1.32 1.18 2.02
TMED6 ENST00000288025 61.16 64.25 63.99 0.62 0.49 0.52 1.32 1.20 1.38
SRCIN1 ENST00000264659 61.17 4.82 31.21 0.62 3.29 0.85 1.32 0.31 1.56
HINT2 ENST00000259667 61.17 86.11 76.74 0.62 0.27 0.34 1.32 0.43 0.60
CA1 ENST00000523953 61.18 84.42 75.80 0.62 0.29 0.38 1.32 0.44 0.63
SLC17A9 ENST00000370351 61.18 77.01 71.65 0.62 0.43 0.44 1.32 0.78 0.83
RERGL ENST00000229002 61.19 85.19 76.30 0.62 0.25 0.37 1.32 0.45 0.61
FAM101A ENST00000324038 61.20 74.97 70.39 0.62 0.53 0.43 1.32 0.93 0.91
WBP1 ENST00000233615 61.20 70.87 67.97 0.62 0.49 0.51 1.32 1.07 1.10
DHRS7 ENST00000216500 61.21 80.67 73.73 0.62 0.37 0.42 1.32 0.56 0.71

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