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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
PDGFRA ENST00000257290 13.31 3.82 5.83 1.67 3.32 3.30 0.66 0.31 0.28
KCNQ1 ENST00000155840 13.31 41.92 25.72 1.66 0.61 1.04 0.67 1.82 1.22
SURF4 ENST00000371989 13.32 27.98 18.64 1.66 1.20 1.59 0.67 1.19 0.81
SLC1A6 ENST00000221742 13.32 20.33 14.54 1.66 1.44 1.99 0.67 0.74 0.59
KLHL5 ENST00000504108 13.33 33.74 21.67 1.66 0.84 1.27 0.67 1.56 0.91
NRD1 ENST00000354831 13.33 17.36 12.89 1.66 1.59 2.10 0.67 0.75 0.53
NPTX1 ENST00000306773 13.34 23.81 16.37 1.66 1.38 1.71 0.67 0.93 0.68
RAB5B ENST00000360299 13.34 42.26 25.94 1.66 0.61 1.00 0.67 1.88 1.24
DIRAS2 ENST00000375765 13.35 41.77 25.65 1.66 0.61 1.06 0.67 1.78 1.21
KDM6A ENST00000377967 13.35 3.95 5.92 1.66 3.28 3.29 0.67 0.32 0.29
HS3ST5 ENST00000312719 13.36 38.36 23.90 1.66 0.75 1.09 0.67 1.71 1.04
ELOF1 ENST00000252445 13.36 72.99 41.39 1.66 0.51 0.73 0.67 1.03 2.02
IPCEF1 ENST00000422970 13.37 36.04 22.88 1.66 0.80 1.19 0.67 1.58 0.97
IGF2BP2 ENST00000382199 13.37 20.98 14.94 1.67 1.44 1.90 0.67 0.83 0.63
ZNF462 ENST00000277225 13.38 0.39 4.18 1.67 4.13 3.78 0.67 0.28 0.23
RAB1B ENST00000311481 13.38 22.50 15.76 1.68 1.51 1.77 0.67 0.84 0.66
FAM171B ENST00000304698 13.39 18.88 13.78 1.68 1.53 2.09 0.67 0.76 0.57
CDK5R2 ENST00000302625 13.39 30.51 19.97 1.68 1.09 1.47 0.67 1.37 0.85
EIF5B ENST00000289371 13.40 9.01 8.54 1.68 2.43 2.52 0.67 0.47 0.37
BBX ENST00000325805 13.40 17.46 13.02 1.67 1.58 2.09 0.67 0.74 0.52
STIP1 ENST00000305218 13.41 5.83 6.97 1.67 2.86 2.90 0.67 0.35 0.33
EIF5 ENST00000216554 13.41 11.19 9.81 1.67 2.09 2.29 0.67 0.54 0.40
PRKAR2B ENST00000265717 13.42 2.80 5.44 1.67 3.52 3.44 0.67 0.28 0.26
ST8SIA3 ENST00000324000 13.42 19.71 14.25 1.67 1.43 2.01 0.67 0.74 0.60
PDE6D ENST00000287600 13.43 56.16 32.95 1.67 0.52 0.86 0.67 1.55 1.67

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