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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
CLK1 ENST00000434813 29.06 41.89 33.63 1.10 0.61 0.90 1.54 1.82 1.72
MIS12 ENST00000381165 29.06 58.24 41.87 1.10 0.54 0.68 1.54 1.43 2.01
SREBF2 ENST00000361204 29.07 16.05 20.66 1.10 1.82 1.47 1.54 0.68 0.88
AUP1 ENST00000377526 29.07 44.33 34.86 1.10 0.61 0.90 1.54 1.95 1.75
RUNDC1 ENST00000361677 29.08 32.87 29.15 1.10 0.82 0.84 1.54 1.44 1.32
LRTM2 ENST00000543818 29.08 20.20 22.77 1.10 1.43 1.19 1.54 0.75 0.98
GPI ENST00000415930 29.09 36.77 31.10 1.10 0.76 0.84 1.54 1.65 1.52
FRMD6 ENST00000344768 29.09 25.41 25.36 1.10 1.25 1.05 1.54 1.05 1.17
GMPPA ENST00000358215 29.10 50.14 37.86 1.10 0.67 0.85 1.54 1.99 2.01
ARHGAP30 ENST00000368013 29.10 6.25 15.48 1.10 2.73 1.81 1.54 0.36 0.67
GLOD4 ENST00000301329 29.11 81.62 54.91 1.10 0.33 0.51 1.54 0.52 1.73
LCAT ENST00000264005 29.12 31.97 28.69 1.10 0.92 0.80 1.54 1.48 1.34
KRT19 ENST00000361566 29.12 39.49 32.49 1.10 0.70 0.89 1.54 1.63 1.62
ZNF624 ENST00000311331 29.13 24.17 24.70 1.10 1.33 1.05 1.54 0.98 1.09
STK31 ENST00000355870 29.13 21.14 23.22 1.10 1.47 1.19 1.54 0.82 1.01
DGAT1 ENST00000332324 29.14 66.98 46.78 1.10 0.53 0.67 1.55 1.24 1.87
RPL29 ENST00000466397 29.14 49.57 37.60 1.10 0.66 0.82 1.55 2.02 2.01
MAPKAPK3 ENST00000446044 29.15 60.65 43.26 1.10 0.53 0.65 1.55 1.41 1.99
PTRF ENST00000357037 29.15 57.97 41.79 1.10 0.56 0.72 1.55 1.45 2.01
SPOCK2 ENST00000373109 29.16 23.26 24.23 1.10 1.43 1.13 1.55 0.92 1.05
MLX ENST00000246912 29.16 35.42 30.52 1.10 0.77 0.80 1.55 1.55 1.47
MAK16 ENST00000360128 29.17 14.05 19.62 1.10 2.07 1.53 1.55 0.59 0.85
H2AFJ ENST00000544848 29.17 72.53 49.81 1.10 0.47 0.65 1.55 1.04 1.89
GBA2 ENST00000378103 29.18 54.26 40.05 1.10 0.62 0.82 1.55 1.70 1.99
MNX1 ENST00000252971 29.18 25.27 25.33 1.10 1.29 1.05 1.55 1.02 1.17

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