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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
DBP ENST00000222122 22.60 46.17 32.60 1.46 0.73 0.87 1.05 2.04 1.63
CCDC93 ENST00000376300 22.61 31.23 24.96 1.46 1.00 1.02 1.05 1.37 1.14
UBA3 ENST00000361055 22.61 17.04 17.74 1.44 1.62 1.67 1.05 0.74 0.78
MPZ ENST00000533357 22.62 35.04 27.00 1.44 0.76 1.00 1.05 1.58 1.28
CYGB ENST00000293230 22.62 46.53 32.76 1.44 0.73 0.86 1.04 2.02 1.65
SLC9A7 ENST00000328306 22.63 9.97 13.97 1.44 2.33 2.05 1.04 0.50 0.59
RAB31 ENST00000578921 22.63 62.12 40.57 1.44 0.54 0.81 1.05 1.35 2.04
UBASH3B ENST00000284273 22.64 30.69 24.74 1.44 1.05 1.05 1.05 1.38 1.10
BMP5 ENST00000370830 22.64 37.80 28.41 1.44 0.80 0.78 1.05 1.70 1.29
GLMN ENST00000370360 22.65 49.52 34.37 1.44 0.65 0.87 1.05 2.03 1.77
ASTN1 ENST00000361833 22.65 6.50 12.15 1.44 2.63 2.29 1.05 0.37 0.49
CD37 ENST00000323906 22.66 62.28 40.65 1.46 0.53 0.81 1.04 1.33 2.05
NFASC ENST00000339876 22.66 6.74 12.29 1.46 2.67 2.25 1.03 0.37 0.50
SPTSSB ENST00000359175 22.67 94.12 58.47 1.46 0.25 0.51 1.04 0.25 1.65
SACM1L ENST00000389061 22.67 17.50 18.00 1.46 1.58 1.70 1.04 0.73 0.78
PLCE1 ENST00000371380 22.68 21.71 20.26 1.46 1.46 1.48 1.04 0.81 0.88
CHMP1A ENST00000397901 22.68 63.56 41.34 1.46 0.51 0.73 1.04 1.25 2.01
SPECC1L ENST00000314328 22.69 14.36 16.33 1.47 2.04 1.71 1.04 0.61 0.67
PPIL4 ENST00000253329 22.70 47.77 33.39 1.47 0.59 0.87 1.04 1.99 1.72
SLC31A1 ENST00000374212 22.70 53.25 36.09 1.46 0.66 0.89 1.04 1.73 1.80
TNFRSF21 ENST00000296861 22.71 30.17 24.47 1.46 1.10 1.08 1.04 1.41 1.08
P2RX3 ENST00000263314 22.71 51.04 35.05 1.46 0.65 0.86 1.04 1.92 1.75
LTBP1 ENST00000404816 22.72 23.03 21.00 1.46 1.44 1.43 1.04 0.91 0.88
TNFSF8 ENST00000223795 22.72 14.58 16.48 1.46 2.04 1.71 1.04 0.61 0.69
RNF125 ENST00000217740 22.73 69.78 44.90 1.44 0.54 0.68 1.05 1.13 2.03

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