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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
KTN1 ENST00000395314 47.65 16.41 30.21 0.54 1.81 0.81 1.80 0.69 1.44
BAG3 ENST00000369085 47.66 22.76 33.36 0.54 1.46 0.87 1.80 0.89 1.72
NDE1 ENST00000396355 47.66 36.71 40.45 0.54 0.77 0.80 1.80 1.66 2.02
INADL ENST00000371158 47.67 56.66 51.23 0.54 0.53 0.63 1.80 1.55 1.92
NIN ENST00000382041 47.67 19.71 31.88 0.54 1.43 0.91 1.80 0.74 1.58
PNKD ENST00000273077 47.68 55.93 50.86 0.53 0.49 0.67 1.80 1.56 1.84
ZNF8 ENST00000196548 47.68 37.49 40.76 0.53 0.78 0.81 1.80 1.67 2.04
ZNF8 ENST00000608843 47.69 37.52 40.75 0.53 0.78 0.81 1.80 1.66 2.04
ANKEF1 ENST00000378380 47.69 50.53 47.96 0.53 0.63 0.67 1.80 1.95 1.88
LY75 ENST00000554112 47.70 50.21 47.81 0.53 0.67 0.65 1.80 1.99 1.89
LY75-CD302 ENST00000504764 47.70 50.21 47.82 0.53 0.67 0.65 1.80 1.99 1.89
PLEKHG7 ENST00000344636 47.71 80.05 65.43 0.53 0.37 0.53 1.80 0.60 1.31
HESX1 ENST00000295934 47.71 67.49 57.57 0.53 0.54 0.51 1.80 1.20 1.66
TIMM44 ENST00000270538 47.72 31.21 37.69 0.53 1.00 0.82 1.80 1.37 2.01
TBL2 ENST00000305632 47.72 47.09 46.12 0.53 0.67 0.67 1.80 2.00 1.97
SIDT1 ENST00000264852 47.73 47.08 46.10 0.53 0.67 0.67 1.80 1.99 1.96
ZNF684 ENST00000372699 47.74 78.75 64.60 0.53 0.42 0.51 1.80 0.73 1.32
EXOSC10 ENST00000376936 47.74 39.53 41.85 0.53 0.68 0.68 1.80 1.63 2.02
FREM2 ENST00000280481 47.75 23.86 33.98 0.53 1.39 0.90 1.80 0.95 1.73
VAMP5 ENST00000306384 47.75 88.92 70.65 0.53 0.25 0.43 1.80 0.35 0.89
SMAD9 ENST00000379826 47.76 47.15 46.15 0.53 0.66 0.67 1.80 1.99 1.97
SLC25A33 ENST00000302692 47.76 38.66 41.44 0.53 0.70 0.73 1.80 1.66 2.02
SCG5 ENST00000300175 47.77 67.29 57.46 0.53 0.56 0.51 1.80 1.21 1.66
PDGFA ENST00000354513 47.77 24.27 34.30 0.53 1.30 0.87 1.80 0.99 1.77
CYB5R4 ENST00000369681 47.78 51.56 48.56 0.53 0.62 0.67 1.80 1.87 1.85

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