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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
CDH12 ENST00000382254 36.16 28.24 30.40 0.95 1.18 0.81 1.81 1.22 1.46
SYN3 ENST00000358763 36.17 30.33 31.48 0.95 1.08 0.86 1.81 1.41 1.56
PRELP ENST00000343110 36.17 71.10 53.05 0.95 0.49 0.61 1.82 1.07 1.87
GREB1 ENST00000381486 36.18 23.56 28.06 0.96 1.39 0.82 1.82 0.93 1.28
YIPF3 ENST00000372422 36.18 31.25 31.91 0.96 1.00 0.91 1.82 1.37 1.57
DNAJB12 ENST00000338820 36.19 24.37 28.46 0.97 1.32 0.78 1.82 1.00 1.29
TTYH2 ENST00000269346 36.19 34.78 33.65 0.97 0.77 0.90 1.82 1.55 1.72
ASCC1 ENST00000342444 36.20 76.97 56.38 0.97 0.43 0.51 1.82 0.79 1.73
EIF3F ENST00000533626 36.20 13.32 22.92 0.97 2.05 1.19 1.82 0.61 0.98
HSPB8 ENST00000281938 36.21 64.29 49.17 0.97 0.49 0.72 1.81 1.20 1.84
PTPLAD1 ENST00000261875 36.21 29.43 31.04 0.97 1.09 0.82 1.81 1.38 1.51
ANXA5 ENST00000296511 36.22 73.77 54.57 0.97 0.53 0.56 1.82 1.03 1.73
LPAR6 ENST00000378434 36.22 69.36 52.00 0.97 0.56 0.62 1.82 1.14 1.94
GCGR ENST00000400723 36.23 47.30 40.08 0.97 0.67 0.82 1.82 2.00 1.98
SLC50A1 ENST00000368404 36.23 58.64 46.13 0.97 0.54 0.67 1.82 1.42 1.97
RSPO2 ENST00000276659 36.24 43.64 38.23 0.97 0.62 0.85 1.82 1.97 2.04
CECR6 ENST00000331437 36.24 30.00 31.35 0.97 1.09 0.87 1.82 1.42 1.55
SH3PXD2B ENST00000311601 36.25 24.35 28.49 0.97 1.32 0.78 1.82 1.00 1.29
MB ENST00000397326 36.25 72.56 53.84 0.97 0.47 0.62 1.82 1.04 1.78
JUND ENST00000252818 36.26 40.11 36.31 0.97 0.63 0.85 1.82 1.71 1.87
NUP153 ENST00000262077 36.26 4.02 18.09 0.97 3.25 1.67 1.82 0.32 0.78
FAM151B ENST00000282226 36.27 78.60 57.36 0.97 0.40 0.51 1.82 0.74 1.67
KLC2 ENST00000417856 36.27 14.35 23.40 0.97 2.04 1.19 1.82 0.61 1.00
INPP5J ENST00000404390 36.28 64.89 49.50 0.97 0.48 0.67 1.82 1.24 1.84
YTHDF1 ENST00000370339 36.28 8.09 20.25 0.97 2.52 1.48 1.82 0.44 0.88

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