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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
CEP19 ENST00000409690 47.91 66.18 56.89 0.54 0.53 0.51 1.80 1.20 1.70
CDK10 ENST00000353379 47.92 76.52 63.35 0.54 0.42 0.48 1.80 0.83 1.36
CCNDBP1 ENST00000300213 47.92 38.96 41.66 0.54 0.70 0.72 1.80 1.64 2.01
HEATR6 ENST00000184956 47.93 48.10 46.73 0.54 0.63 0.66 1.80 1.99 1.87
HIBCH ENST00000359678 47.93 65.33 56.43 0.54 0.51 0.52 1.80 1.25 1.72
SORBS2 ENST00000355634 47.94 18.63 31.50 0.54 1.48 0.86 1.80 0.75 1.57
CFP ENST00000247153 47.94 25.67 35.00 0.54 1.24 0.87 1.80 1.05 1.73
MMP13 ENST00000260302 47.95 80.45 65.79 0.54 0.37 0.51 1.80 0.59 1.26
ACAD11 ENST00000264990 47.95 47.82 46.54 0.54 0.59 0.66 1.80 1.99 1.90
SLC6A20 ENST00000358525 47.96 69.79 58.98 0.54 0.54 0.49 1.80 1.13 1.65
DOCK1 ENST00000280333 47.96 14.15 29.20 0.54 2.07 0.84 1.80 0.59 1.33
CHRNA2 ENST00000407991 47.97 67.46 57.70 0.54 0.54 0.49 1.80 1.20 1.68
SEC22C ENST00000264454 47.97 66.34 57.02 0.54 0.54 0.51 1.80 1.20 1.70
PCGF6 ENST00000369847 47.98 48.34 46.88 0.54 0.63 0.68 1.81 2.00 1.88
NYNRIN ENST00000382554 47.98 29.65 37.06 0.54 1.10 0.80 1.81 1.39 1.95
NDUFA4 ENST00000339600 47.99 76.14 63.17 0.54 0.43 0.49 1.81 0.87 1.37
TRIM29 ENST00000341846 47.99 50.51 48.11 0.54 0.63 0.66 1.81 1.95 1.88
CHAT ENST00000337653 48.00 48.40 46.92 0.54 0.63 0.70 1.80 2.01 1.87
GNB3 ENST00000229264 48.00 75.54 62.69 0.54 0.44 0.51 1.80 0.90 1.39
CAPG ENST00000263867 48.01 76.53 63.41 0.54 0.42 0.49 1.80 0.83 1.37
DTX2 ENST00000324432 48.01 30.31 37.39 0.54 1.08 0.85 1.80 1.41 2.00
FAM63A ENST00000361738 48.02 70.62 59.64 0.54 0.51 0.49 1.80 1.09 1.69
SMUG1 ENST00000508394 48.02 59.13 52.95 0.54 0.49 0.61 1.80 1.44 1.87
AATF ENST00000225402 48.03 55.32 50.75 0.54 0.57 0.66 1.80 1.61 1.84
ALOX5 ENST00000374391 48.03 32.48 38.56 0.54 0.86 0.85 1.80 1.48 2.02

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