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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
FAM196B ENST00000377365 74.90 11.50 41.43 0.38 2.11 0.73 0.78 0.57 2.02
SPACA3 ENST00000269053 74.90 65.45 72.94 0.38 0.53 0.40 0.78 1.25 0.81
TRAF3IP1 ENST00000373327 74.91 37.40 55.83 0.38 0.76 0.52 0.78 1.66 1.75
DEFB127 ENST00000382388 74.91 86.65 84.06 0.38 0.24 0.35 0.78 0.40 0.42
C6orf58 ENST00000329722 74.92 71.31 76.17 0.38 0.53 0.37 0.78 1.07 0.62
ZNF232 ENST00000250076 74.92 51.36 64.42 0.38 0.63 0.51 0.78 1.89 1.33
ECH1 ENST00000221418 74.93 61.88 70.74 0.38 0.57 0.43 0.78 1.35 0.86
CYP1A2 ENST00000343932 74.93 73.94 77.64 0.38 0.53 0.38 0.78 1.02 0.55
ADI1 ENST00000327435 74.94 82.40 82.04 0.38 0.34 0.35 0.78 0.52 0.46
OR1L8 ENST00000304865 74.94 73.21 77.24 0.38 0.54 0.35 0.78 1.02 0.58
PEX10 ENST00000288774 74.95 50.62 64.05 0.38 0.63 0.52 0.78 1.95 1.38
SLC17A3 ENST00000397060 74.95 76.44 78.99 0.38 0.43 0.39 0.78 0.85 0.53
ALKBH7 ENST00000245812 74.96 82.72 82.21 0.38 0.33 0.35 0.78 0.50 0.44
CCDC17 ENST00000528266 74.97 75.56 78.50 0.38 0.44 0.38 0.77 0.90 0.54
STPG2 ENST00000295268 74.97 78.88 80.24 0.38 0.40 0.37 0.77 0.71 0.51
TMEM139 ENST00000359333 74.98 72.67 76.95 0.38 0.47 0.37 0.77 1.04 0.61
ASGR1 ENST00000269299 74.98 87.23 84.44 0.38 0.20 0.33 0.77 0.41 0.40
KANK3 ENST00000330915 74.99 59.25 69.20 0.38 0.49 0.44 0.77 1.43 0.99
GBP1 ENST00000370473 74.99 68.97 74.90 0.38 0.54 0.39 0.77 1.15 0.64
KIF19 ENST00000389916 75.00 55.82 67.21 0.38 0.52 0.52 0.77 1.58 1.16
PLEKHG6 ENST00000396988 75.00 56.39 67.50 0.38 0.52 0.51 0.77 1.53 1.14
FOXB2 ENST00000376708 75.01 80.17 80.93 0.38 0.37 0.39 0.77 0.59 0.51
NPY4R ENST00000374312 75.01 83.86 82.83 0.38 0.28 0.32 0.77 0.47 0.42
CLEC1B ENST00000298527 75.02 77.11 79.35 0.38 0.42 0.39 0.77 0.78 0.54
DYDC1 ENST00000372204 75.02 62.03 70.88 0.38 0.56 0.43 0.77 1.37 0.86

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