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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
NAPEPLD ENST00000417955 51.41 50.61 50.00 0.59 0.63 0.62 1.87 1.95 1.90
ARAP2 ENST00000303965 51.41 28.63 38.32 0.59 1.18 0.85 1.87 1.29 2.04
TCF7L1 ENST00000282111 35.01 21.68 26.43 0.92 1.46 1.01 1.87 0.81 1.25
LGI4 ENST00000310123 35.01 35.76 33.54 0.92 0.78 0.87 1.87 1.58 1.72
RAB13 ENST00000368575 35.02 40.38 35.79 0.92 0.61 0.85 1.87 1.76 1.78
ABHD6 ENST00000478253 35.02 53.73 42.66 0.92 0.63 0.68 1.87 1.70 2.02
LANCL2 ENST00000254770 35.07 24.38 27.88 0.92 1.30 0.85 1.87 1.00 1.29
PHGDH ENST00000369409 35.08 41.84 36.58 0.92 0.61 0.85 1.87 1.80 1.91
MTMR14 ENST00000296003 35.22 35.62 33.58 0.92 0.78 0.87 1.87 1.58 1.72
DNAJC10 ENST00000264065 35.23 32.85 32.25 0.92 0.84 0.90 1.87 1.44 1.60
FBXO31 ENST00000311635 35.32 22.07 26.87 0.92 1.49 0.97 1.87 0.81 1.27
TAF10 ENST00000299424 35.32 21.95 26.79 0.92 1.47 0.96 1.87 0.81 1.28
ZNF263 ENST00000219069 35.37 53.32 42.62 0.95 0.66 0.67 1.87 1.72 2.02
TLN2 ENST00000561311 35.38 10.59 21.13 0.96 2.15 1.42 1.87 0.51 0.90
PSMD6 ENST00000295901 35.39 7.97 19.70 0.96 2.54 1.53 1.87 0.44 0.85
PFKFB3 ENST00000379775 35.40 22.11 26.93 0.96 1.52 0.99 1.87 0.83 1.27
GRAMD2 ENST00000309731 35.40 73.38 53.83 0.96 0.54 0.62 1.87 1.03 1.79
LEPROTL1 ENST00000523116 35.41 39.58 35.63 0.96 0.68 0.85 1.87 1.65 1.77
NDUFS1 ENST00000455934 35.95 43.86 38.18 0.94 0.61 0.85 1.87 1.97 2.04
BCL7C ENST00000215115 35.96 43.45 37.94 0.94 0.61 0.85 1.87 1.95 2.02
BMPER ENST00000297161 35.97 34.19 33.21 0.94 0.84 0.87 1.87 1.55 1.68
CPLX4 ENST00000299721 35.97 89.24 63.89 0.94 0.27 0.51 1.87 0.36 1.39
TMEM87B ENST00000283206 35.98 52.38 42.44 0.94 0.62 0.68 1.87 1.82 2.01
ZMYND10 ENST00000231749 35.98 46.84 39.77 0.94 0.71 0.80 1.87 1.97 2.04
ZCCHC3 ENST00000382352 35.99 64.33 49.06 0.94 0.49 0.72 1.87 1.20 1.83

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