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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
TRIM67 ENST00000366653 31.77 14.68 21.33 0.96 1.99 1.37 1.71 0.62 0.91
TMEM67 ENST00000453321 31.78 50.53 39.49 0.96 0.63 0.80 1.71 1.95 2.03
S100B ENST00000291700 31.78 86.60 59.46 0.96 0.24 0.49 1.70 0.40 1.70
SNX17 ENST00000233575 31.79 29.76 28.90 0.96 1.13 0.81 1.71 1.40 1.31
BOC ENST00000495514 31.79 29.92 29.02 0.96 1.11 0.82 1.72 1.41 1.31
GSN ENST00000373818 31.80 45.43 36.81 0.96 0.68 0.82 1.72 2.00 1.94
HOXB4 ENST00000332503 31.80 59.44 44.03 0.96 0.52 0.62 1.72 1.41 2.03
C9orf72 ENST00000380003 31.81 43.59 35.79 0.96 0.62 0.85 1.72 1.95 1.78
TTK ENST00000369798 31.81 23.02 25.53 0.96 1.44 1.05 1.72 0.91 1.19
RAD51C ENST00000337432 31.82 77.52 54.18 0.96 0.42 0.59 1.72 0.79 1.73
FUZ ENST00000313777 31.82 43.85 35.96 0.96 0.61 0.86 1.72 1.97 1.77
SOX30 ENST00000265007 31.83 9.63 18.75 0.96 2.47 1.57 1.72 0.50 0.83
KLB ENST00000257408 31.83 21.18 24.58 0.96 1.46 1.06 1.72 0.81 1.10
SRPK1 ENST00000373825 31.84 32.26 30.23 0.96 0.86 0.82 1.72 1.46 1.44
B3GALTL ENST00000343307 31.84 73.87 52.10 0.96 0.53 0.61 1.72 1.03 1.93
PPIP5K1 ENST00000420765 31.85 30.56 29.38 0.96 1.08 0.84 1.72 1.39 1.36
LYSMD3 ENST00000315948 31.85 32.79 30.56 0.96 0.84 0.80 1.72 1.44 1.47
INPP5K ENST00000421807 31.86 41.66 34.94 0.96 0.62 0.90 1.72 1.81 1.75
CDC7 ENST00000428239 31.86 39.54 33.87 0.96 0.68 0.89 1.72 1.64 1.73
LRCH1 ENST00000389797 31.87 5.15 16.32 0.96 3.21 1.71 1.72 0.32 0.67
ITGB7 ENST00000267082 31.87 34.83 31.55 0.95 0.76 0.86 1.72 1.55 1.56
ISG20L2 ENST00000313146 31.88 39.36 33.78 0.95 0.70 0.89 1.72 1.65 1.74
EPAS1 ENST00000263734 31.88 18.19 23.13 0.95 1.49 1.20 1.72 0.75 1.00
STAT2 ENST00000314128 31.89 14.51 21.29 0.95 2.04 1.39 1.72 0.61 0.91
PGP ENST00000333503 31.89 42.43 35.38 0.95 0.59 0.87 1.72 1.89 1.77

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