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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
AGBL5 ENST00000360131 25.06 36.52 28.94 1.38 0.78 0.81 1.13 1.63 1.31
HNRNPAB ENST00000358344 25.06 20.85 21.10 1.38 1.42 1.42 1.13 0.84 0.90
TSC22D2 ENST00000361875 25.07 13.77 17.28 1.38 2.06 1.64 1.14 0.60 0.74
GNL1 ENST00000376621 25.07 7.66 14.05 1.38 2.49 2.04 1.14 0.42 0.60
SMC2 ENST00000286398 25.08 7.87 14.20 1.38 2.54 1.99 1.14 0.44 0.60
LHFPL2 ENST00000380345 25.08 55.09 38.38 1.38 0.57 0.84 1.15 1.63 2.04
PDCL ENST00000259467 25.09 33.42 27.38 1.38 0.84 0.96 1.15 1.52 1.27
TANC2 ENST00000424789 25.09 3.41 11.85 1.38 3.42 2.24 1.15 0.28 0.45
CHRNB2 ENST00000368476 25.10 43.77 32.63 1.37 0.61 0.87 1.15 1.95 1.63
CHTF8 ENST00000448552 25.10 57.13 39.45 1.37 0.56 0.77 1.15 1.50 2.05
MYOG ENST00000241651 25.11 19.78 20.57 1.37 1.42 1.48 1.15 0.74 0.88
SLC29A2 ENST00000357440 25.11 75.84 49.34 1.37 0.43 0.70 1.15 0.88 1.84
TBC1D24 ENST00000293970 25.12 61.99 41.78 1.37 0.56 0.72 1.15 1.36 2.01
TMEM121 ENST00000392519 25.12 33.70 27.53 1.37 0.84 0.96 1.15 1.56 1.27
HIGD1A ENST00000452906 25.13 69.50 46.03 1.37 0.54 0.68 1.15 1.12 1.97
PPP1R12A ENST00000450142 25.13 2.17 11.32 1.37 3.65 2.19 1.15 0.29 0.45
PPIE ENST00000372830 25.14 21.91 21.67 1.37 1.46 1.27 1.15 0.81 0.91
DIO2 ENST00000555750 25.14 20.89 21.15 1.37 1.42 1.42 1.15 0.84 0.90
ETNK2 ENST00000367202 25.15 61.76 41.69 1.38 0.57 0.72 1.15 1.37 2.01
PIGU ENST00000217446 25.15 45.89 33.70 1.38 0.75 0.90 1.15 2.02 1.73
EFEMP2 ENST00000307998 25.16 30.84 26.14 1.38 1.08 0.99 1.15 1.36 1.27
KIAA0196 ENST00000318410 25.16 39.86 30.78 1.38 0.65 0.78 1.15 1.69 1.49
HOXD3 ENST00000468418 25.17 27.65 24.46 1.38 1.27 1.08 1.15 1.18 1.08
SRRT ENST00000347433 25.17 17.83 19.48 1.38 1.52 1.54 1.15 0.72 0.84
PSMB5 ENST00000361611 25.18 12.05 16.41 1.37 2.06 1.71 1.15 0.57 0.68

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