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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
BNIP2 ENST00000267859 47.14 45.98 45.26 0.56 0.76 0.70 1.82 2.02 2.00
GNL2 ENST00000373062 47.14 28.65 36.00 0.56 1.19 0.87 1.82 1.29 1.79
TMPRSS6 ENST00000346753 47.15 37.88 40.71 0.56 0.80 0.81 1.82 1.70 2.04
TMEM106C ENST00000429772 47.15 76.74 62.99 0.56 0.40 0.51 1.82 0.83 1.39
LPXN ENST00000528954 47.16 50.85 47.86 0.57 0.63 0.65 1.82 1.92 1.89
HSD3B7 ENST00000297679 47.16 76.50 62.79 0.57 0.42 0.48 1.82 0.83 1.39
MRPL52 ENST00000355151 47.17 88.99 70.38 0.57 0.25 0.43 1.82 0.35 0.91
PCDH8 ENST00000377942 47.17 33.71 38.70 0.57 0.84 0.82 1.82 1.56 2.02
ARMC12 ENST00000288065 47.18 57.68 51.59 0.57 0.56 0.62 1.82 1.48 1.94
DCLRE1C ENST00000378278 47.18 36.65 40.20 0.57 0.77 0.82 1.82 1.66 2.00
FKBP3 ENST00000216330 47.19 55.07 50.11 0.57 0.58 0.63 1.82 1.63 1.90
ATG10 ENST00000282185 47.19 73.64 61.01 0.57 0.52 0.43 1.82 1.03 1.56
AKAP4 ENST00000358526 47.20 8.84 26.19 0.57 2.47 0.99 1.82 0.48 1.25
GSTO2 ENST00000338595 47.20 83.32 67.00 0.57 0.27 0.52 1.82 0.47 1.19
GPALPP1 ENST00000361121 47.21 56.53 50.93 0.57 0.52 0.66 1.82 1.54 1.85
SYT16 ENST00000430451 47.21 40.08 41.88 0.57 0.63 0.68 1.82 1.70 2.01
WIPF2 ENST00000323571 47.22 28.27 35.86 0.56 1.19 0.86 1.82 1.22 1.79
ECHS1 ENST00000368547 47.22 51.29 48.13 0.56 0.65 0.66 1.82 1.90 1.87
CPLX3 ENST00000395018 47.23 46.13 45.39 0.56 0.73 0.70 1.82 2.04 2.01
IFT57 ENST00000264538 47.23 61.06 53.53 0.56 0.54 0.63 1.82 1.39 1.81
TMEM64 ENST00000458549 47.24 31.21 37.47 0.56 1.00 0.86 1.82 1.37 2.01
KBTBD12 ENST00000405109 47.24 66.36 56.61 0.56 0.54 0.52 1.82 1.20 1.71
CLIP4 ENST00000320081 47.25 43.69 43.84 0.56 0.62 0.61 1.82 1.96 2.02
TCEA3 ENST00000450454 47.25 40.10 41.90 0.56 0.63 0.68 1.82 1.71 2.01
CLUAP1 ENST00000576634 47.26 34.64 39.34 0.56 0.80 0.80 1.83 1.54 2.04

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