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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
AHCYL1 ENST00000369799 1.04 10.62 3.26 4.36 2.14 3.89 0.18 0.51 0.24
FBXL3 ENST00000355619 1.04 11.44 3.63 4.38 2.10 3.84 0.18 0.56 0.23
SNAI2 ENST00000396822 1.05 24.14 10.14 4.37 1.35 2.24 0.18 0.99 0.41
RAB10 ENST00000264710 1.05 10.18 3.06 4.39 2.32 3.94 0.18 0.49 0.23
STAT5B ENST00000293328 1.06 7.66 2.09 4.39 2.51 4.09 0.18 0.42 0.23
MAT2A ENST00000306434 1.06 3.35 0.71 4.40 3.44 4.59 0.18 0.28 0.20
KCNJ6 ENST00000609713 1.07 19.50 7.63 4.40 1.46 2.72 0.18 0.74 0.33
SET ENST00000372692 1.07 4.87 1.14 4.40 3.27 4.39 0.18 0.31 0.21
EEF1A2 ENST00000217182 1.08 4.81 1.12 4.39 3.29 4.41 0.18 0.32 0.21
ATP1A1 ENST00000537345 1.08 1.92 0.36 4.39 3.75 4.80 0.18 0.26 0.18
FAM219A ENST00000445726 1.09 45.39 21.38 4.39 0.68 1.34 0.18 1.99 0.91
ERH ENST00000557016 1.09 19.84 7.83 4.40 1.42 2.62 0.18 0.74 0.35
WDR5 ENST00000358625 1.10 1.95 0.36 4.40 3.75 4.79 0.18 0.25 0.18
NRBP1 ENST00000233557 1.11 2.36 0.46 4.40 3.63 4.73 0.18 0.29 0.17
CREBL2 ENST00000228865 1.11 28.19 12.23 4.39 1.18 2.26 0.18 1.21 0.50
COPS4 ENST00000264389 1.12 5.37 1.29 4.41 3.06 4.37 0.18 0.32 0.21
GABRA2 ENST00000510861 1.12 7.54 2.08 4.41 2.52 4.10 0.18 0.42 0.23
NR4A2 ENST00000339562 1.13 2.24 0.43 4.40 3.65 4.76 0.18 0.30 0.17
MOB4 ENST00000323303 1.13 8.05 2.27 4.40 2.53 4.06 0.17 0.44 0.23
FRG1B ENST00000278882 1.14 52.31 24.76 4.39 0.62 1.04 0.17 1.83 1.10
XPO1 ENST00000401558 1.14 0.12 0.05 4.39 4.10 4.87 0.17 0.28 0.15
PCSK2 ENST00000262545 1.15 5.93 1.56 4.39 2.83 4.30 0.17 0.35 0.23
ELOVL6 ENST00000394607 1.15 14.66 5.18 4.38 2.00 3.59 0.17 0.62 0.26
DCAF7 ENST00000415273 1.16 15.07 5.43 4.38 1.90 3.44 0.17 0.65 0.26
PSMC3 ENST00000298852 1.16 14.57 5.13 4.38 2.04 3.59 0.17 0.61 0.25

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