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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
A1BG ENST00000263100 89.03 64.30 79.99 0.19 0.49 0.35 0.32 1.20 0.52
A1CF ENST00000373995 24.33 47.59 34.17 1.34 0.61 0.89 1.12 2.00 1.75
A2M ENST00000318602 51.33 27.59 37.68 0.59 1.25 0.82 1.84 1.17 2.01
A2ML1 ENST00000299698 71.98 52.10 63.13 0.34 0.61 0.49 0.81 1.85 1.39
A3GALT2 ENST00000442999 87.06 81.31 87.37 0.23 0.33 0.28 0.38 0.54 0.31
A4GALT ENST00000401850 67.21 84.97 79.38 0.59 0.25 0.39 1.03 0.45 0.52
A4GNT ENST00000236709 63.83 39.00 50.44 0.59 0.70 0.67 1.22 1.64 1.89
AAAS ENST00000209873 49.51 55.63 51.71 0.54 0.53 0.62 1.82 1.60 1.94
AACS ENST00000316519 65.50 60.35 64.21 0.57 0.53 0.51 1.10 1.41 1.35
AADAC ENST00000232892 87.24 53.43 73.07 0.23 0.65 0.42 0.38 1.70 0.80
AADACL2 ENST00000356517 85.24 84.81 88.19 0.28 0.27 0.23 0.47 0.42 0.30
AADACL3 ENST00000359318 86.12 85.42 88.91 0.25 0.25 0.19 0.42 0.45 0.28
AADACL4 ENST00000376221 97.04 84.82 93.71 0.10 0.27 0.10 0.11 0.42 0.14
AADAT ENST00000337664 12.32 25.73 16.86 1.68 1.24 1.70 0.61 1.05 0.70
AAED1 ENST00000375234 72.05 90.41 84.58 0.34 0.25 0.34 0.80 0.37 0.40
AAGAB ENST00000261880 72.74 57.42 66.79 0.32 0.54 0.53 0.78 1.49 1.20
AAK1 ENST00000409085 20.68 2.21 8.79 1.56 3.67 2.49 1.00 0.30 0.38
AAMDC ENST00000526415 50.98 88.07 72.18 0.62 0.24 0.43 1.85 0.38 0.82
AAMP ENST00000248450 17.71 19.56 16.45 1.47 1.43 1.72 0.89 0.74 0.69
AANAT ENST00000250615 81.75 69.58 78.96 0.32 0.52 0.39 0.59 1.10 0.52
AAR2 ENST00000373932 33.72 73.37 52.87 0.94 0.54 0.61 1.70 1.03 1.87
AARD ENST00000378279 87.96 61.84 78.14 0.22 0.57 0.39 0.35 1.36 0.55
AARS ENST00000261772 28.30 33.56 29.07 1.18 0.85 0.84 1.49 1.53 1.32
AARS2 ENST00000244571 47.63 46.42 45.73 0.54 0.73 0.67 1.80 2.04 1.98
AARSD1 ENST00000427569 53.09 62.14 57.57 0.63 0.53 0.51 1.78 1.35 1.66

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