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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
GNB4 ENST00000232564 25.18 39.38 30.49 1.37 0.70 0.80 1.15 1.65 1.46
AFTPH ENST00000238855 25.19 2.68 11.60 1.37 3.53 2.23 1.15 0.29 0.45
HOXB8 ENST00000239144 25.19 11.88 16.37 1.37 2.10 1.71 1.15 0.58 0.68
GALK1 ENST00000588479 25.20 60.88 41.26 1.37 0.56 0.75 1.15 1.41 2.01
SCN3B ENST00000392770 25.21 41.73 31.68 1.37 0.61 0.89 1.15 1.79 1.59
HTR1B ENST00000369947 25.21 35.96 28.71 1.37 0.80 0.80 1.15 1.58 1.34
ANO1 ENST00000355303 25.22 13.24 17.09 1.37 2.05 1.66 1.15 0.60 0.72
TBC1D13 ENST00000372648 25.22 34.54 28.08 1.37 0.80 0.81 1.15 1.55 1.29
YIPF4 ENST00000238831 25.23 40.73 31.15 1.37 0.63 0.85 1.16 1.78 1.54
TAF11 ENST00000361288 25.23 44.93 33.23 1.37 0.68 0.87 1.16 1.98 1.68
CAPN6 ENST00000324068 25.24 19.60 20.56 1.37 1.43 1.48 1.17 0.74 0.89
SEH1L ENST00000399892 25.24 19.96 20.75 1.37 1.46 1.46 1.17 0.73 0.89
LGI2 ENST00000382114 25.25 45.32 33.45 1.37 0.68 0.89 1.17 1.98 1.70
PDE1A ENST00000435564 25.25 21.46 21.47 1.37 1.42 1.30 1.17 0.80 0.91
BRD1 ENST00000216267 25.26 8.67 14.73 1.37 2.48 1.95 1.17 0.47 0.62
RBM33 ENST00000401878 25.26 0.12 10.25 1.37 4.11 2.21 1.17 0.28 0.42
ASL ENST00000304874 25.27 49.85 35.68 1.37 0.66 0.85 1.17 2.02 1.76
ANKFN1 ENST00000318698 25.27 40.19 30.94 1.37 0.61 0.80 1.17 1.72 1.51
SERPINF2 ENST00000324015 25.28 32.23 26.93 1.37 0.86 0.99 1.17 1.46 1.27
COLGALT2 ENST00000361927 25.28 46.36 34.00 1.38 0.73 0.90 1.17 2.04 1.72
SALL1 ENST00000251020 25.29 5.34 12.83 1.38 3.11 2.11 1.17 0.32 0.53
GRHPR ENST00000318158 25.29 67.87 45.29 1.38 0.52 0.70 1.17 1.18 2.01
NAB1 ENST00000337386 25.30 29.79 25.61 1.38 1.13 1.05 1.17 1.40 1.21
ZNFX1 ENST00000396105 25.30 9.41 15.14 1.38 2.48 1.86 1.17 0.49 0.64
CLDN11 ENST00000064724 25.31 17.34 19.34 1.38 1.61 1.53 1.17 0.75 0.85

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