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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
GANC ENST00000318010 54.50 66.10 60.92 0.63 0.54 0.43 1.72 1.20 1.58
SLC25A10 ENST00000331531 54.50 63.11 58.93 0.63 0.48 0.49 1.72 1.30 1.65
PSMG2 ENST00000317615 54.51 77.56 67.95 0.63 0.42 0.51 1.72 0.79 1.10
CNGA3 ENST00000393504 54.51 78.31 68.41 0.63 0.43 0.47 1.72 0.74 1.05
TFRC ENST00000360110 54.52 28.53 39.86 0.63 1.15 0.78 1.71 1.27 2.02
SYNGR1 ENST00000328933 54.52 34.97 43.13 0.62 0.76 0.65 1.71 1.56 1.99
MYL4 ENST00000354968 54.53 75.27 66.55 0.62 0.49 0.51 1.71 0.90 1.20
TXNDC15 ENST00000358387 54.53 39.63 45.79 0.62 0.68 0.68 1.71 1.65 1.98
CAMSAP1 ENST00000389532 54.54 8.59 29.75 0.62 2.52 0.86 1.71 0.47 1.42
OR5A1 ENST00000302030 54.54 84.50 72.17 0.62 0.29 0.43 1.71 0.43 0.82
LIPF ENST00000394375 54.55 44.09 48.17 0.62 0.59 0.66 1.71 1.99 1.87
SERPING1 ENST00000278407 54.55 6.01 28.46 0.62 2.82 0.78 1.71 0.35 1.29
GSAP ENST00000257626 54.56 54.32 53.90 0.62 0.62 0.61 1.71 1.68 1.77
MFSD1 ENST00000415822 54.56 69.06 62.75 0.62 0.56 0.48 1.71 1.14 1.39
ANXA6 ENST00000354546 54.57 37.70 44.70 0.62 0.78 0.62 1.71 1.70 2.06
MTHFD2 ENST00000394053 54.57 45.83 49.12 0.62 0.73 0.72 1.71 2.01 1.84
TMEM242 ENST00000400788 54.58 81.50 70.34 0.62 0.33 0.43 1.71 0.54 0.90
DCAF16 ENST00000382247 54.58 77.13 67.71 0.62 0.42 0.52 1.71 0.78 1.12
UNG ENST00000242576 54.59 46.46 49.47 0.62 0.73 0.68 1.71 2.02 1.83
IL17RE ENST00000295980 54.59 40.74 46.35 0.62 0.63 0.67 1.71 1.78 1.89
KRT23 ENST00000209718 54.60 72.50 65.00 0.62 0.47 0.51 1.71 1.03 1.31
TACSTD2 ENST00000371225 54.60 80.31 69.67 0.62 0.37 0.44 1.71 0.58 0.95
MPO ENST00000225275 54.61 63.54 59.32 0.62 0.49 0.51 1.71 1.25 1.69
NBAS ENST00000281513 54.61 40.70 46.35 0.63 0.63 0.67 1.71 1.77 1.90
CHMP1B ENST00000526991 54.62 34.63 42.97 0.63 0.80 0.67 1.71 1.54 2.00

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