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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
CUBN ENST00000377833 58.37 32.57 43.82 0.56 0.86 0.61 1.52 1.48 2.01
GCKR ENST00000264717 58.38 62.69 61.14 0.56 0.51 0.43 1.53 1.31 1.51
NAA11 ENST00000286794 58.38 69.55 65.51 0.56 0.53 0.53 1.53 1.11 1.28
KCNE3 ENST00000310128 58.39 78.36 70.71 0.56 0.43 0.43 1.53 0.73 0.87
TTC3 ENST00000399017 58.39 46.27 51.47 0.56 0.73 0.63 1.52 2.04 1.92
C12orf68 ENST00000316554 58.40 90.13 77.48 0.56 0.25 0.35 1.52 0.38 0.57
C1orf94 ENST00000488417 58.40 31.81 43.48 0.56 0.92 0.62 1.52 1.48 1.99
NEU3 ENST00000294064 58.41 74.84 68.62 0.56 0.53 0.47 1.51 0.95 1.05
OR13C8 ENST00000335040 58.41 90.82 77.81 0.56 0.25 0.38 1.51 0.35 0.54
RAB40B ENST00000571995 58.42 73.62 67.92 0.56 0.52 0.51 1.51 1.03 1.10
OR5AP2 ENST00000302981 58.42 81.81 72.86 0.56 0.34 0.40 1.51 0.51 0.81
SLC9A3 ENST00000264938 58.43 13.23 34.01 0.56 2.05 0.89 1.51 0.60 1.73
RP11-770J1.4 ENST00000532619 58.43 81.67 72.77 0.56 0.33 0.43 1.51 0.52 0.81
CCL28 ENST00000361115 58.44 85.10 74.69 0.56 0.25 0.40 1.51 0.45 0.67
DNAJC9 ENST00000372950 58.44 46.59 51.68 0.56 0.75 0.62 1.51 2.01 1.94
IRX3 ENST00000329734 58.45 21.32 38.17 0.56 1.42 0.85 1.51 0.80 2.04
STX11 ENST00000367568 58.45 73.06 67.58 0.56 0.52 0.51 1.51 1.02 1.14
METTL23 ENST00000341249 58.46 90.64 77.74 0.56 0.25 0.38 1.51 0.36 0.55
PKHD1 ENST00000371117 58.46 35.56 45.69 0.56 0.77 0.68 1.51 1.58 2.00
GPX6 ENST00000361902 58.47 84.02 74.07 0.56 0.27 0.38 1.51 0.45 0.69
SYNJ2 ENST00000355585 58.47 36.77 46.28 0.57 0.76 0.67 1.51 1.65 1.92
RPS27L ENST00000330964 58.48 72.64 67.34 0.57 0.47 0.52 1.52 1.04 1.15
IL12RB2 ENST00000262345 58.48 36.12 46.01 0.57 0.81 0.68 1.52 1.60 1.96
NDUFAF7 ENST00000002125 58.49 81.21 72.52 0.57 0.35 0.46 1.52 0.55 0.83
SLC5A10 ENST00000395647 58.49 56.48 57.41 0.57 0.52 0.51 1.52 1.54 1.67

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