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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
C15orf62 ENST00000344320 37.32 69.04 52.48 0.95 0.54 0.61 1.72 1.14 1.92
UBE3B ENST00000342494 37.33 27.58 30.76 0.95 1.25 0.78 1.72 1.17 1.49
TMPPE ENST00000342462 37.33 67.19 51.38 0.94 0.54 0.63 1.72 1.22 1.90
SDHB ENST00000375499 37.34 42.19 38.04 0.94 0.61 0.85 1.72 1.87 2.02
GNG11 ENST00000248564 37.34 67.38 51.51 0.94 0.56 0.63 1.72 1.20 1.92
PDGFD ENST00000393158 37.35 37.83 35.72 0.94 0.80 0.85 1.72 1.70 1.77
DCLK3 ENST00000416516 37.35 30.53 32.14 0.94 1.09 0.90 1.72 1.38 1.60
HOXB6 ENST00000484302 37.36 67.59 51.62 0.94 0.53 0.62 1.72 1.19 1.92
TMEM116 ENST00000552374 37.36 75.75 56.34 0.94 0.43 0.49 1.73 0.88 1.75
SCN4A ENST00000435607 37.37 14.62 24.03 0.94 2.01 1.10 1.73 0.61 1.06
NAA40 ENST00000377793 37.37 72.17 54.28 0.94 0.52 0.59 1.73 1.04 1.73
DUSP4 ENST00000240100 37.38 10.08 21.86 0.94 2.33 1.21 1.73 0.49 0.95
FHL5 ENST00000326771 37.38 84.65 61.75 0.94 0.27 0.46 1.73 0.42 1.46
PARP11 ENST00000228820 37.39 67.43 51.56 0.94 0.56 0.62 1.74 1.20 1.93
GFI1B ENST00000339463 37.39 48.01 40.90 0.94 0.63 0.78 1.74 2.00 2.06
RANBP6 ENST00000259569 37.40 29.47 31.65 0.94 1.10 0.89 1.74 1.39 1.58
ARHGAP24 ENST00000395184 37.41 43.24 38.61 0.94 0.62 0.84 1.75 1.92 2.01
CDAN1 ENST00000356231 37.41 36.72 35.27 0.94 0.77 0.86 1.75 1.66 1.76
C2CD3 ENST00000313663 37.42 33.31 33.52 0.94 0.84 0.89 1.75 1.51 1.72
ADAMTS9 ENST00000498707 37.42 18.69 26.22 0.92 1.52 1.00 1.75 0.75 1.26
CALCOCO2 ENST00000448105 37.43 35.06 34.47 0.92 0.76 0.90 1.75 1.58 1.77
GDE1 ENST00000353258 37.43 64.26 49.80 0.92 0.49 0.65 1.75 1.20 1.89
CYB5R1 ENST00000367249 37.44 72.06 54.29 0.92 0.52 0.59 1.75 1.03 1.73
FRMPD3 ENST00000276185 37.44 24.27 29.03 0.92 1.30 0.82 1.75 0.99 1.31
TAL1 ENST00000294339 37.45 36.73 35.31 0.92 0.76 0.87 1.75 1.66 1.75

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