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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
TSPAN11 ENST00000261177 73.86 71.74 75.81 0.35 0.51 0.38 0.81 1.07 0.63
CHGB ENST00000378961 73.87 41.93 57.92 0.35 0.61 0.48 0.81 1.82 1.66
AGBL1 ENST00000441037 73.88 63.48 71.12 0.35 0.49 0.43 0.81 1.25 0.86
IFNLR1 ENST00000327535 73.88 39.99 56.76 0.35 0.63 0.52 0.81 1.69 1.70
C5orf49 ENST00000399810 73.89 86.36 83.48 0.35 0.25 0.33 0.81 0.43 0.40
NOL8 ENST00000545558 73.89 41.85 57.91 0.35 0.61 0.48 0.81 1.80 1.66
CABP2 ENST00000294288 73.90 53.77 65.36 0.35 0.63 0.53 0.81 1.71 1.32
MRPL20 ENST00000344843 73.90 88.01 84.25 0.35 0.25 0.34 0.81 0.38 0.42
ZNF529 ENST00000591340 73.91 47.18 61.15 0.35 0.66 0.43 0.81 2.00 1.50
CCDC130 ENST00000586600 73.91 40.85 57.27 0.35 0.61 0.51 0.81 1.78 1.70
OR4L1 ENST00000315683 73.92 78.33 79.41 0.35 0.43 0.39 0.81 0.74 0.52
AQPEP ENST00000357872 73.92 47.93 61.65 0.35 0.59 0.46 0.81 1.99 1.47
DNAJC15 ENST00000379221 73.93 93.89 87.11 0.35 0.25 0.28 0.81 0.26 0.30
QSOX2 ENST00000358701 73.93 41.73 57.86 0.35 0.61 0.49 0.81 1.79 1.66
OR1S2 ENST00000302592 73.94 93.80 87.07 0.35 0.27 0.28 0.81 0.26 0.30
HS1BP3 ENST00000304031 73.94 68.42 73.98 0.35 0.52 0.39 0.81 1.21 0.70
USP6 ENST00000574788 73.95 53.67 65.29 0.35 0.63 0.53 0.81 1.70 1.31
ASB13 ENST00000357700 73.95 86.37 83.52 0.35 0.25 0.33 0.81 0.42 0.40
TDRD6 ENST00000316081 73.96 66.26 72.85 0.35 0.53 0.42 0.81 1.20 0.81
SDF2L1 ENST00000248958 73.96 56.38 66.89 0.35 0.52 0.53 0.81 1.53 1.20
YY1AP1 ENST00000368339 73.97 67.89 73.74 0.35 0.52 0.42 0.81 1.17 0.71
KLHL17 ENST00000338591 73.97 69.68 74.73 0.35 0.53 0.40 0.81 1.12 0.67
CDHR2 ENST00000510636 73.98 46.12 60.60 0.35 0.75 0.44 0.81 2.04 1.58
ALG10B ENST00000308742 73.98 73.49 76.86 0.35 0.53 0.35 0.81 1.03 0.61
NUDT18 ENST00000309188 73.99 83.88 82.30 0.35 0.28 0.34 0.81 0.46 0.45

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