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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
GGCT ENST00000275428 24.80 71.22 46.71 1.39 0.53 0.66 1.12 1.06 1.86
STRIP2 ENST00000249344 24.80 48.74 34.95 1.39 0.63 0.90 1.12 1.99 1.75
PDE12 ENST00000311180 24.81 30.66 25.86 1.39 1.05 1.01 1.12 1.38 1.23
AQP4 ENST00000383168 24.81 52.47 36.84 1.39 0.66 0.81 1.12 1.84 1.94
CUL9 ENST00000252050 24.82 11.09 15.77 1.38 2.09 1.76 1.12 0.53 0.66
MLLT11 ENST00000368921 24.82 67.73 44.91 1.38 0.52 0.68 1.12 1.19 2.04
C1GALT1C1 ENST00000304661 24.83 26.33 23.66 1.38 1.19 1.16 1.12 1.08 1.02
YAF2 ENST00000442791 24.83 27.95 24.44 1.38 1.20 1.08 1.12 1.19 1.08
SEC24B ENST00000265175 24.84 5.52 12.73 1.38 3.01 2.16 1.12 0.33 0.52
PIK3CG ENST00000359195 24.84 30.44 25.75 1.38 1.09 1.04 1.12 1.38 1.22
TRPC4AP ENST00000252015 24.85 16.42 18.61 1.38 1.80 1.58 1.13 0.69 0.81
FBXO33 ENST00000298097 24.85 8.36 14.33 1.37 2.52 2.00 1.13 0.46 0.60
DNAJC27 ENST00000264711 24.86 47.61 34.46 1.37 0.62 0.90 1.13 1.99 1.75
GOLGB1 ENST00000393667 24.86 19.08 20.00 1.37 1.52 1.48 1.14 0.76 0.85
ZNF460 ENST00000360338 24.87 41.44 31.37 1.37 0.62 0.87 1.14 1.81 1.55
RNF111 ENST00000559209 24.87 6.65 13.36 1.37 2.64 2.05 1.14 0.36 0.55
MSL3 ENST00000312196 24.88 4.45 12.28 1.37 3.27 2.25 1.14 0.32 0.50
LRRC16A ENST00000329474 24.89 16.98 18.91 1.37 1.63 1.54 1.14 0.73 0.83
SP1 ENST00000327443 24.89 1.10 10.59 1.37 4.03 2.16 1.13 0.28 0.44
LPIN2 ENST00000261596 24.90 24.64 22.92 1.37 1.30 1.19 1.12 1.05 0.98
SCARB2 ENST00000264896 24.90 37.24 29.22 1.38 0.76 0.82 1.12 1.66 1.34
TPK1 ENST00000360057 24.91 37.29 29.26 1.38 0.76 0.84 1.12 1.66 1.34
KRR1 ENST00000229214 24.91 31.24 26.24 1.38 1.00 1.01 1.12 1.37 1.26
C20orf194 ENST00000252032 24.92 30.57 25.88 1.38 1.08 1.01 1.12 1.39 1.23
SORCS3 ENST00000369701 24.92 21.90 21.54 1.38 1.46 1.28 1.12 0.81 0.92

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