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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
ZSCAN23 ENST00000289788 31.51 74.67 52.36 0.95 0.54 0.61 1.69 0.96 1.90
DAAM2 ENST00000398904 31.52 0.93 13.91 0.95 4.10 2.09 1.69 0.29 0.59
ARHGAP6 ENST00000337414 31.52 7.34 17.29 0.95 2.54 1.64 1.69 0.37 0.74
ACTR10 ENST00000254286 31.53 35.23 31.59 0.95 0.76 0.89 1.69 1.58 1.58
ITGAL ENST00000356798 31.53 19.19 23.47 0.95 1.49 1.19 1.69 0.76 1.00
METAP1D ENST00000315796 31.54 57.70 42.95 0.95 0.57 0.67 1.69 1.48 2.00
HECTD3 ENST00000372172 31.54 19.99 23.83 0.95 1.44 1.10 1.69 0.73 1.04
STX6 ENST00000258301 31.55 40.56 34.35 0.95 0.63 0.87 1.69 1.76 1.77
CCDC91 ENST00000545336 31.55 42.91 35.43 0.95 0.62 0.87 1.70 1.92 1.77
NCF2 ENST00000367535 31.56 39.13 33.50 0.95 0.70 0.89 1.70 1.62 1.72
ZNF341 ENST00000342427 31.56 34.06 31.02 0.95 0.82 0.82 1.70 1.55 1.52
LYST ENST00000389794 31.57 11.69 19.66 0.95 2.10 1.53 1.70 0.57 0.85
PELO ENST00000274311 31.57 50.63 39.42 0.95 0.63 0.78 1.70 1.95 2.04
RWDD1 ENST00000466444 31.58 18.34 23.08 0.95 1.49 1.20 1.70 0.74 1.00
TMEM60 ENST00000257663 31.58 32.40 30.17 0.95 0.87 0.81 1.70 1.47 1.45
GAL3ST1 ENST00000402321 31.59 28.20 28.09 0.95 1.18 0.81 1.70 1.21 1.29
SLC24A4 ENST00000532405 31.59 45.48 36.71 0.95 0.70 0.82 1.70 1.99 1.93
BBS2 ENST00000245157 31.60 55.93 41.99 0.95 0.49 0.68 1.70 1.56 1.99
BMP1 ENST00000306385 31.60 22.77 25.26 0.95 1.46 1.05 1.70 0.89 1.15
VGF ENST00000249330 31.61 25.32 26.64 0.95 1.28 0.99 1.70 1.03 1.25
RIMS2 ENST00000406091 31.62 6.29 16.81 0.95 2.71 1.70 1.70 0.36 0.70
IL23A ENST00000228534 31.62 37.13 32.58 0.95 0.80 0.87 1.70 1.66 1.63
ETFDH ENST00000511912 31.63 55.11 41.61 0.95 0.58 0.72 1.70 1.63 2.00
JRKL ENST00000458427 31.63 44.52 36.19 0.95 0.63 0.87 1.70 1.98 1.84
C1orf43 ENST00000368521 31.64 42.45 35.24 0.95 0.59 0.86 1.70 1.89 1.76

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