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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
TBCD ENST00000355528 69.60 23.68 45.34 0.54 1.39 0.70 0.97 0.93 1.99
TTC39B ENST00000512701 69.61 52.13 61.60 0.54 0.61 0.46 0.97 1.85 1.48
ADCK2 ENST00000072869 69.61 49.74 60.11 0.54 0.66 0.48 0.97 2.02 1.61
MAL ENST00000309988 69.62 25.81 46.39 0.54 1.21 0.67 0.97 1.06 1.90
RAB3IL1 ENST00000394836 69.62 42.84 55.91 0.54 0.62 0.49 0.97 1.91 1.75
TAPBP ENST00000426633 69.63 65.12 69.56 0.54 0.49 0.44 0.98 1.24 0.96
B4GALNT2 ENST00000300404 69.63 73.97 74.71 0.54 0.53 0.40 0.98 1.02 0.67
PRSS45 ENST00000442359 69.64 84.45 80.37 0.54 0.29 0.38 0.98 0.44 0.50
RP11-108K14.8 ENST00000468317 69.65 42.42 55.72 0.54 0.59 0.53 0.97 1.89 1.74
TBC1D16 ENST00000310924 69.65 32.45 50.04 0.54 0.86 0.61 0.97 1.48 1.92
FAM219B ENST00000357635 69.66 88.15 82.26 0.54 0.24 0.35 0.97 0.38 0.45
NRSN2 ENST00000382291 69.66 85.29 80.77 0.54 0.25 0.39 0.97 0.46 0.52
SCN7A ENST00000409855 69.67 42.10 55.55 0.53 0.61 0.52 0.97 1.85 1.73
C1orf106 ENST00000413687 69.67 40.05 54.41 0.53 0.63 0.57 0.96 1.70 1.75
COL23A1 ENST00000390654 69.68 46.89 58.33 0.53 0.71 0.49 0.96 1.94 1.64
LYG2 ENST00000333017 69.68 93.18 84.78 0.53 0.28 0.34 0.96 0.30 0.40
HAUS5 ENST00000203166 69.69 37.27 52.78 0.53 0.76 0.61 0.96 1.66 1.88
MRPL4 ENST00000253099 69.69 77.74 76.85 0.53 0.42 0.35 0.96 0.79 0.61
ZNF621 ENST00000339296 69.70 58.76 65.81 0.53 0.54 0.51 0.96 1.43 1.25
SVOPL ENST00000419765 69.70 54.55 63.22 0.53 0.59 0.49 0.96 1.66 1.36
LEPREL2 ENST00000396725 69.71 57.91 65.28 0.53 0.57 0.53 0.96 1.46 1.31
TMEM259 ENST00000356663 69.71 8.16 37.22 0.53 2.56 0.81 0.95 0.44 1.98
HABP2 ENST00000351270 69.72 67.56 71.08 0.53 0.53 0.43 0.95 1.20 0.86
VNN1 ENST00000367928 69.72 60.11 66.59 0.53 0.52 0.52 0.95 1.39 1.21
CHRDL2 ENST00000263671 69.73 49.02 59.71 0.53 0.66 0.49 0.95 2.03 1.66

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